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Showing NP-Card for Variapeptin (NP0011694)

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Record Information
Version2.0
Created at2021-01-05 21:18:26 UTC
Updated at2021-07-15 17:09:39 UTC
NP-MRD IDNP0011694
Secondary Accession NumbersNone
Natural Product Identification
Common NameVariapeptin
Provided ByNPAtlasNPAtlas Logo
DescriptionVariapeptin belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating. Variapeptin is found in Streptomyces variabilis. Variapeptin was first documented in 1990 (PMID: 2358400). Based on a literature review very few articles have been published on Variapeptin.
Structure
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MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0011694 (Variapeptin)


  Mrv1652307012121553D          

139143  0  0  0  0            999 V2000
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M  END
Download

3D MOL for NP0011694 (Variapeptin)

     RDKit          3D

139143  0  0  0  0  0  0  0  0999 V2000
   12.7369   -0.1253   -1.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0011694 (Variapeptin)


  Mrv1652307012121553D          

139143  0  0  0  0            999 V2000
   12.7369   -0.1253   -1.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0011694

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]ON1C(=O)[C@@]2([H])N(N([H])C([H])([H])C([H])([H])C2([H])[H])C(=O)[C@]([H])(N([H])C(=O)[C@@](O[H])(C([H])([H])[H])[C@@]2(O[H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(C([H])([H])[C@]([H])(C([H])([H])[H])C([H])([H])C([H])([H])[H])C([H])([H])C2([H])[H])[C@@]([H])(OC(=O)[C@@]([H])(N([H])C(=O)[C@@]2([H])N(N([H])C([H])([H])C([H])([H])C2([H])[H])C(=O)[C@]([H])(N(C(=O)[C@@]1([H])C([H])([H])[H])C([H])([H])[H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H])C([H])([H])O[H])C([H])(C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C46H72N8O13/c1-9-27(4)23-31-19-20-46(64,67-29(31)6)45(7,63)44(62)50-36-37(26(2)3)66-43(61)32(25-55)49-38(56)33-17-13-21-47-52(33)40(58)35(24-30-15-11-10-12-16-30)51(8)39(57)28(5)54(65)41(59)34-18-14-22-48-53(34)42(36)60/h10-12,15-16,26-29,31-37,47-48,55,63-65H,9,13-14,17-25H2,1-8H3,(H,49,56)(H,50,62)/t27-,28-,29+,31+,32+,33+,34+,35-,36-,37+,45+,46+/m1/s1

> <INCHI_KEY>
PBXKWAYVRNEWSB-UHFFFAOYSA-N

> <FORMULA>
C46H72N8O13

> <MOLECULAR_WEIGHT>
945.125

> <EXACT_MASS>
944.52188441

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
139

> <JCHEM_AVERAGE_POLARIZABILITY>
99.22950139562262

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-N-[(3R,6R,9S,17S,20S,23S)-3-benzyl-7-hydroxy-20-(hydroxymethyl)-4,6-dimethyl-2,5,8,15,19,22-hexaoxo-17-(propan-2-yl)-18-oxa-1,4,7,13,14,21,27-heptaazatricyclo[21.4.0.0^{9,14}]heptacosan-16-yl]-2-hydroxy-2-[(2S,5S,6S)-2-hydroxy-6-methyl-5-[(2R)-2-methylbutyl]oxan-2-yl]propanamide

> <ALOGPS_LOGP>
1.44

> <JCHEM_LOGP>
0.9359814699999993

> <ALOGPS_LOGS>
-3.90

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.582808726247679

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.674259892478021

> <JCHEM_PKA_STRONGEST_BASIC>
4.334292702151487

> <JCHEM_POLAR_SURFACE_AREA>
279.95000000000005

> <JCHEM_REFRACTIVITY>
261.76219999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.18e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-N-[(3R,6R,9S,17S,20S,23S)-3-benzyl-7-hydroxy-20-(hydroxymethyl)-17-isopropyl-4,6-dimethyl-2,5,8,15,19,22-hexaoxo-18-oxa-1,4,7,13,14,21,27-heptaazatricyclo[21.4.0.0^{9,14}]heptacosan-16-yl]-2-hydroxy-2-[(2S,5S,6S)-2-hydroxy-6-methyl-5-[(2R)-2-methylbutyl]oxan-2-yl]propanamide

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0011694 (Variapeptin)

     RDKit          3D

139143  0  0  0  0  0  0  0  0999 V2000
   12.7369   -0.1253   -1.2387 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0162   -0.7232   -2.4069 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.5033   -0.3222   -2.3709 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.9828   -1.0289   -3.6361 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8828   -0.9280   -1.1728 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4883   -0.6989   -0.8199 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.3820   -1.0708   -1.7160 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2304   -0.0818   -1.6072 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9305    0.4196   -0.2588 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.2911    1.6879   -0.4123 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0707   -0.3559    0.6424 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.5699   -1.7473    1.0097 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0409    0.3184    1.9000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6584   -0.5686    0.1968 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4913   -0.9151   -0.9754 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6239   -0.3644    1.1380 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1938   -0.5245    0.8436 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7015   -1.8516    1.1445 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6604   -2.7240    0.8511 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4126   -2.4803    1.6252 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3106   -3.3335    2.7701 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8316   -2.6109    3.8662 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2113   -2.1347    3.6325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6368   -1.8549    2.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8119   -2.4984    1.1649 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.9545   -2.0532   -0.1976 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8713   -2.1383   -0.8991 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0479   -1.5495   -0.8935 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8540   -0.9467   -2.1373 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4406   -1.5733   -0.4942 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.9143   -3.0041   -0.2575 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3311   -1.0362   -1.5548 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1212   -1.4550   -2.7377 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3817   -0.1106   -1.3761 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8541    0.6535   -2.5469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0345    0.1457   -0.1455 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.4290   -0.5177   -0.2194 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3623   -1.9652   -0.4258 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2881   -2.8013    0.6737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2394   -4.1660    0.5195 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2634   -4.7451   -0.7358 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3372   -3.9277   -1.8388 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3858   -2.5433   -1.6689 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1985    1.5761    0.2138 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9496    1.7411    1.2598 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6897    2.7113   -0.3804 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6469    3.6947   -0.7996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1507    4.3920   -1.9453 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9474    5.2682   -1.5652 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3162    4.6238   -0.3589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3261    3.1038   -0.6471 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.3268    2.5266    0.2492 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5613    2.6620    1.5071 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1520    1.8488   -0.0771 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2129    2.1089   -1.1153 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8966    3.5653   -1.3530 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3942    4.0930   -0.1683 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9251    1.3196   -0.9450 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3996    1.1211   -2.1087 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5466    0.9706    0.2504 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4446    0.7032    1.1406 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0316    0.9283    2.5649 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7182    2.2779    2.5831 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1347    1.1007    3.5441 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0889    0.7551    0.4654 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2470    0.7165   -0.3013 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.3946    1.0506    0.6268 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4241    0.9254   -1.0282 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8163   -0.1793   -1.4421 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5479   -0.7065   -0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4143   -0.3098   -3.3367 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.0844   -1.8282   -2.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4684    0.7556   -2.4611 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3158   -0.3466   -4.1916 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8481   -1.1701   -4.3780 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6340   -2.0382   -3.4529 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5157   -0.6341   -0.2782 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.0530   -2.0681   -1.1782 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3398   -1.3198    0.1599 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0075   -2.1240   -1.5601 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6842   -1.0440   -2.7683 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5744    0.8196   -2.2153 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3571   -0.4386   -2.1392 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4675    2.2303    0.3874 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8048   -2.1033    1.7796 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5100   -1.7367    1.5629 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4747   -2.4805    0.2020 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4750    1.1110    1.7599 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8731   -0.0914    2.0969 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2362   -0.5519   -0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5888   -3.7727    2.8663 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8651   -3.2454    4.8167 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1743   -1.7465    4.1204 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3196   -1.1610    4.2095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9820   -2.7981    4.1173 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6196   -0.7352    2.0961 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7216   -2.1786    2.1589 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1603   -3.5977    1.1703 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1077   -1.3610   -2.6144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6457   -0.9749    0.3946 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4119   -3.1248    0.7290 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6402   -3.3479   -1.0212 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0520   -3.7272   -0.3579 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6533    1.3504   -2.3010 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9438    1.1037   -2.9932 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2285   -0.0694   -3.3238 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5442   -0.4181    0.7048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9460   -0.2692    0.7523 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0198    0.0209   -0.9881 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2647   -2.3885    1.6907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1807   -4.8370    1.3745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2267   -5.8187   -0.8718 H   0  0  0  0  0  0  0  0  0  0  0  0
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    9.1498    1.9437    1.2617 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6255    0.2323    1.3343 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0011694 (Variapeptin)

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0      12.737  -0.125  -1.239  0.00  0.00           C+0
HETATM    2  C   UNK     0      12.016  -0.723  -2.407  0.00  0.00           C+0
HETATM    3  C   UNK     0      10.503  -0.322  -2.371  0.00  0.00           C+0
HETATM    4  C   UNK     0       9.983  -1.029  -3.636  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.883  -0.928  -1.173  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.488  -0.699  -0.820  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.382  -1.071  -1.716  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.230  -0.082  -1.607  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.931   0.420  -0.259  0.00  0.00           C+0
HETATM   10  O   UNK     0       5.291   1.688  -0.412  0.00  0.00           O+0
HETATM   11  C   UNK     0       5.071  -0.356   0.642  0.00  0.00           C+0
HETATM   12  C   UNK     0       5.570  -1.747   1.010  0.00  0.00           C+0
HETATM   13  O   UNK     0       5.041   0.318   1.900  0.00  0.00           O+0
HETATM   14  C   UNK     0       3.658  -0.569   0.197  0.00  0.00           C+0
HETATM   15  O   UNK     0       3.491  -0.915  -0.975  0.00  0.00           O+0
HETATM   16  N   UNK     0       2.624  -0.364   1.138  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.194  -0.525   0.844  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.702  -1.852   1.145  0.00  0.00           C+0
HETATM   19  O   UNK     0       1.660  -2.724   0.851  0.00  0.00           O+0
HETATM   20  N   UNK     0      -0.413  -2.480   1.625  0.00  0.00           N+0
HETATM   21  N   UNK     0      -0.311  -3.333   2.770  0.00  0.00           N+0
HETATM   22  C   UNK     0      -0.832  -2.611   3.866  0.00  0.00           C+0
HETATM   23  C   UNK     0      -2.211  -2.135   3.632  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.637  -1.855   2.224  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.812  -2.498   1.165  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.954  -2.053  -0.198  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.871  -2.138  -0.899  0.00  0.00           O+0
HETATM   28  N   UNK     0      -3.048  -1.550  -0.894  0.00  0.00           N+0
HETATM   29  O   UNK     0      -2.854  -0.947  -2.137  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.441  -1.573  -0.494  0.00  0.00           C+0
HETATM   31  C   UNK     0      -4.914  -3.004  -0.258  0.00  0.00           C+0
HETATM   32  C   UNK     0      -5.331  -1.036  -1.555  0.00  0.00           C+0
HETATM   33  O   UNK     0      -5.121  -1.455  -2.738  0.00  0.00           O+0
HETATM   34  N   UNK     0      -6.382  -0.111  -1.376  0.00  0.00           N+0
HETATM   35  C   UNK     0      -6.854   0.654  -2.547  0.00  0.00           C+0
HETATM   36  C   UNK     0      -7.035   0.146  -0.146  0.00  0.00           C+0
HETATM   37  C   UNK     0      -8.429  -0.518  -0.219  0.00  0.00           C+0
HETATM   38  C   UNK     0      -8.362  -1.965  -0.426  0.00  0.00           C+0
HETATM   39  C   UNK     0      -8.288  -2.801   0.674  0.00  0.00           C+0
HETATM   40  C   UNK     0      -8.239  -4.166   0.520  0.00  0.00           C+0
HETATM   41  C   UNK     0      -8.263  -4.745  -0.736  0.00  0.00           C+0
HETATM   42  C   UNK     0      -8.337  -3.928  -1.839  0.00  0.00           C+0
HETATM   43  C   UNK     0      -8.386  -2.543  -1.669  0.00  0.00           C+0
HETATM   44  C   UNK     0      -7.199   1.576   0.214  0.00  0.00           C+0
HETATM   45  O   UNK     0      -7.950   1.741   1.260  0.00  0.00           O+0
HETATM   46  N   UNK     0      -6.690   2.711  -0.380  0.00  0.00           N+0
HETATM   47  N   UNK     0      -7.647   3.695  -0.800  0.00  0.00           N+0
HETATM   48  C   UNK     0      -7.151   4.392  -1.945  0.00  0.00           C+0
HETATM   49  C   UNK     0      -5.947   5.268  -1.565  0.00  0.00           C+0
HETATM   50  C   UNK     0      -5.316   4.624  -0.359  0.00  0.00           C+0
HETATM   51  C   UNK     0      -5.326   3.104  -0.647  0.00  0.00           C+0
HETATM   52  C   UNK     0      -4.327   2.527   0.249  0.00  0.00           C+0
HETATM   53  O   UNK     0      -4.561   2.662   1.507  0.00  0.00           O+0
HETATM   54  N   UNK     0      -3.152   1.849  -0.077  0.00  0.00           N+0
HETATM   55  C   UNK     0      -2.213   2.109  -1.115  0.00  0.00           C+0
HETATM   56  C   UNK     0      -1.897   3.565  -1.353  0.00  0.00           C+0
HETATM   57  O   UNK     0      -1.394   4.093  -0.168  0.00  0.00           O+0
HETATM   58  C   UNK     0      -0.925   1.320  -0.945  0.00  0.00           C+0
HETATM   59  O   UNK     0      -0.400   1.121  -2.109  0.00  0.00           O+0
HETATM   60  O   UNK     0      -0.547   0.971   0.250  0.00  0.00           O+0
HETATM   61  C   UNK     0       0.445   0.703   1.141  0.00  0.00           C+0
HETATM   62  C   UNK     0       0.032   0.928   2.565  0.00  0.00           C+0
HETATM   63  C   UNK     0      -0.718   2.278   2.583  0.00  0.00           C+0
HETATM   64  C   UNK     0       1.135   1.101   3.544  0.00  0.00           C+0
HETATM   65  O   UNK     0       7.089   0.755   0.465  0.00  0.00           O+0
HETATM   66  C   UNK     0       8.247   0.717  -0.301  0.00  0.00           C+0
HETATM   67  C   UNK     0       9.395   1.051   0.627  0.00  0.00           C+0
HETATM   68  H   UNK     0      12.424   0.925  -1.028  0.00  0.00           H+0
HETATM   69  H   UNK     0      13.816  -0.179  -1.442  0.00  0.00           H+0
HETATM   70  H   UNK     0      12.548  -0.707  -0.308  0.00  0.00           H+0
HETATM   71  H   UNK     0      12.414  -0.310  -3.337  0.00  0.00           H+0
HETATM   72  H   UNK     0      12.084  -1.828  -2.345  0.00  0.00           H+0
HETATM   73  H   UNK     0      10.468   0.756  -2.461  0.00  0.00           H+0
HETATM   74  H   UNK     0       9.316  -0.347  -4.192  0.00  0.00           H+0
HETATM   75  H   UNK     0      10.848  -1.170  -4.378  0.00  0.00           H+0
HETATM   76  H   UNK     0       9.634  -2.038  -3.453  0.00  0.00           H+0
HETATM   77  H   UNK     0      10.516  -0.634  -0.278  0.00  0.00           H+0
HETATM   78  H   UNK     0      10.053  -2.068  -1.178  0.00  0.00           H+0
HETATM   79  H   UNK     0       8.340  -1.320   0.160  0.00  0.00           H+0
HETATM   80  H   UNK     0       7.008  -2.124  -1.560  0.00  0.00           H+0
HETATM   81  H   UNK     0       7.684  -1.044  -2.768  0.00  0.00           H+0
HETATM   82  H   UNK     0       6.574   0.820  -2.215  0.00  0.00           H+0
HETATM   83  H   UNK     0       5.357  -0.439  -2.139  0.00  0.00           H+0
HETATM   84  H   UNK     0       5.468   2.230   0.387  0.00  0.00           H+0
HETATM   85  H   UNK     0       4.805  -2.103   1.780  0.00  0.00           H+0
HETATM   86  H   UNK     0       6.510  -1.737   1.563  0.00  0.00           H+0
HETATM   87  H   UNK     0       5.475  -2.481   0.202  0.00  0.00           H+0
HETATM   88  H   UNK     0       4.475   1.111   1.760  0.00  0.00           H+0
HETATM   89  H   UNK     0       2.873  -0.091   2.097  0.00  0.00           H+0
HETATM   90  H   UNK     0       1.236  -0.552  -0.308  0.00  0.00           H+0
HETATM   91  H   UNK     0       0.589  -3.773   2.866  0.00  0.00           H+0
HETATM   92  H   UNK     0      -0.865  -3.245   4.817  0.00  0.00           H+0
HETATM   93  H   UNK     0      -0.174  -1.746   4.120  0.00  0.00           H+0
HETATM   94  H   UNK     0      -2.320  -1.161   4.210  0.00  0.00           H+0
HETATM   95  H   UNK     0      -2.982  -2.798   4.117  0.00  0.00           H+0
HETATM   96  H   UNK     0      -2.620  -0.735   2.096  0.00  0.00           H+0
HETATM   97  H   UNK     0      -3.722  -2.179   2.159  0.00  0.00           H+0
HETATM   98  H   UNK     0      -2.160  -3.598   1.170  0.00  0.00           H+0
HETATM   99  H   UNK     0      -2.108  -1.361  -2.614  0.00  0.00           H+0
HETATM  100  H   UNK     0      -4.646  -0.975   0.395  0.00  0.00           H+0
HETATM  101  H   UNK     0      -5.412  -3.125   0.729  0.00  0.00           H+0
HETATM  102  H   UNK     0      -5.640  -3.348  -1.021  0.00  0.00           H+0
HETATM  103  H   UNK     0      -4.052  -3.727  -0.358  0.00  0.00           H+0
HETATM  104  H   UNK     0      -7.653   1.350  -2.301  0.00  0.00           H+0
HETATM  105  H   UNK     0      -5.944   1.104  -2.993  0.00  0.00           H+0
HETATM  106  H   UNK     0      -7.229  -0.069  -3.324  0.00  0.00           H+0
HETATM  107  H   UNK     0      -6.544  -0.418   0.705  0.00  0.00           H+0
HETATM  108  H   UNK     0      -8.946  -0.269   0.752  0.00  0.00           H+0
HETATM  109  H   UNK     0      -9.020   0.021  -0.988  0.00  0.00           H+0
HETATM  110  H   UNK     0      -8.265  -2.389   1.691  0.00  0.00           H+0
HETATM  111  H   UNK     0      -8.181  -4.837   1.375  0.00  0.00           H+0
HETATM  112  H   UNK     0      -8.227  -5.819  -0.872  0.00  0.00           H+0
HETATM  113  H   UNK     0      -8.358  -4.354  -2.832  0.00  0.00           H+0
HETATM  114  H   UNK     0      -8.446  -1.967  -2.578  0.00  0.00           H+0
HETATM  115  H   UNK     0      -7.911   4.306  -0.020  0.00  0.00           H+0
HETATM  116  H   UNK     0      -6.766   3.659  -2.693  0.00  0.00           H+0
HETATM  117  H   UNK     0      -7.944   4.993  -2.419  0.00  0.00           H+0
HETATM  118  H   UNK     0      -6.355   6.270  -1.356  0.00  0.00           H+0
HETATM  119  H   UNK     0      -5.205   5.305  -2.393  0.00  0.00           H+0
HETATM  120  H   UNK     0      -4.343   4.996  -0.073  0.00  0.00           H+0
HETATM  121  H   UNK     0      -6.008   4.799   0.514  0.00  0.00           H+0
HETATM  122  H   UNK     0      -5.127   2.929  -1.716  0.00  0.00           H+0
HETATM  123  H   UNK     0      -2.906   1.001   0.537  0.00  0.00           H+0
HETATM  124  H   UNK     0      -2.733   1.794  -2.076  0.00  0.00           H+0
HETATM  125  H   UNK     0      -2.785   4.148  -1.642  0.00  0.00           H+0
HETATM  126  H   UNK     0      -1.069   3.678  -2.098  0.00  0.00           H+0
HETATM  127  H   UNK     0      -2.155   4.124   0.480  0.00  0.00           H+0
HETATM  128  H   UNK     0       1.228   1.534   1.008  0.00  0.00           H+0
HETATM  129  H   UNK     0      -0.689   0.228   2.975  0.00  0.00           H+0
HETATM  130  H   UNK     0      -0.721   2.639   3.656  0.00  0.00           H+0
HETATM  131  H   UNK     0      -1.774   2.148   2.320  0.00  0.00           H+0
HETATM  132  H   UNK     0      -0.164   3.041   2.034  0.00  0.00           H+0
HETATM  133  H   UNK     0       1.883   1.794   3.153  0.00  0.00           H+0
HETATM  134  H   UNK     0       1.522   0.172   4.002  0.00  0.00           H+0
HETATM  135  H   UNK     0       0.687   1.653   4.431  0.00  0.00           H+0
HETATM  136  H   UNK     0       8.181   1.400  -1.154  0.00  0.00           H+0
HETATM  137  H   UNK     0      10.262   1.351  -0.007  0.00  0.00           H+0
HETATM  138  H   UNK     0       9.150   1.944   1.262  0.00  0.00           H+0
HETATM  139  H   UNK     0       9.626   0.232   1.334  0.00  0.00           H+0
CONECT    1    2   68   69   70                                             
CONECT    2    1    3   71   72                                             
CONECT    3    2    4    5   73                                             
CONECT    4    3   74   75   76                                             
CONECT    5    3    6   77   78                                             
CONECT    6    5    7   66   79                                             
CONECT    7    6    8   80   81                                             
CONECT    8    7    9   82   83                                             
CONECT    9    8   10   11   65                                             
CONECT   10    9   84                                                       
CONECT   11    9   12   13   14                                             
CONECT   12   11   85   86   87                                             
CONECT   13   11   88                                                       
CONECT   14   11   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   89                                                  
CONECT   17   16   18   61   90                                             
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   25                                                  
CONECT   21   20   22   91                                                  
CONECT   22   21   23   92   93                                             
CONECT   23   22   24   94   95                                             
CONECT   24   23   25   96   97                                             
CONECT   25   24   26   20   98                                             
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29   30                                                  
CONECT   29   28   99                                                       
CONECT   30   28   31   32  100                                             
CONECT   31   30  101  102  103                                             
CONECT   32   30   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35   36                                                  
CONECT   35   34  104  105  106                                             
CONECT   36   34   37   44  107                                             
CONECT   37   36   38  108  109                                             
CONECT   38   37   39   43                                                  
CONECT   39   38   40  110                                                  
CONECT   40   39   41  111                                                  
CONECT   41   40   42  112                                                  
CONECT   42   41   43  113                                                  
CONECT   43   42   38  114                                                  
CONECT   44   36   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47   51                                                  
CONECT   47   46   48  115                                                  
CONECT   48   47   49  116  117                                             
CONECT   49   48   50  118  119                                             
CONECT   50   49   51  120  121                                             
CONECT   51   50   52   46  122                                             
CONECT   52   51   53   54                                                  
CONECT   53   52                                                            
CONECT   54   52   55  123                                                  
CONECT   55   54   56   58  124                                             
CONECT   56   55   57  125  126                                             
CONECT   57   56  127                                                       
CONECT   58   55   59   60                                                  
CONECT   59   58                                                            
CONECT   60   58   61                                                       
CONECT   61   60   62   17  128                                             
CONECT   62   61   63   64  129                                             
CONECT   63   62  130  131  132                                             
CONECT   64   62  133  134  135                                             
CONECT   65    9   66                                                       
CONECT   66   65   67    6  136                                             
CONECT   67   66  137  138  139                                             
CONECT   68    1                                                            
CONECT   69    1                                                            
CONECT   70    1                                                            
CONECT   71    2                                                            
CONECT   72    2                                                            
CONECT   73    3                                                            
CONECT   74    4                                                            
CONECT   75    4                                                            
CONECT   76    4                                                            
CONECT   77    5                                                            
CONECT   78    5                                                            
CONECT   79    6                                                            
CONECT   80    7                                                            
CONECT   81    7                                                            
CONECT   82    8                                                            
CONECT   83    8                                                            
CONECT   84   10                                                            
CONECT   85   12                                                            
CONECT   86   12                                                            
CONECT   87   12                                                            
CONECT   88   13                                                            
CONECT   89   16                                                            
CONECT   90   17                                                            
CONECT   91   21                                                            
CONECT   92   22                                                            
CONECT   93   22                                                            
CONECT   94   23                                                            
CONECT   95   23                                                            
CONECT   96   24                                                            
CONECT   97   24                                                            
CONECT   98   25                                                            
CONECT   99   29                                                            
CONECT  100   30                                                            
CONECT  101   31                                                            
CONECT  102   31                                                            
CONECT  103   31                                                            
CONECT  104   35                                                            
CONECT  105   35                                                            
CONECT  106   35                                                            
CONECT  107   36                                                            
CONECT  108   37                                                            
CONECT  109   37                                                            
CONECT  110   39                                                            
CONECT  111   40                                                            
CONECT  112   41                                                            
CONECT  113   42                                                            
CONECT  114   43                                                            
CONECT  115   47                                                            
CONECT  116   48                                                            
CONECT  117   48                                                            
CONECT  118   49                                                            
CONECT  119   49                                                            
CONECT  120   50                                                            
CONECT  121   50                                                            
CONECT  122   51                                                            
CONECT  123   54                                                            
CONECT  124   55                                                            
CONECT  125   56                                                            
CONECT  126   56                                                            
CONECT  127   57                                                            
CONECT  128   61                                                            
CONECT  129   62                                                            
CONECT  130   63                                                            
CONECT  131   63                                                            
CONECT  132   63                                                            
CONECT  133   64                                                            
CONECT  134   64                                                            
CONECT  135   64                                                            
CONECT  136   66                                                            
CONECT  137   67                                                            
CONECT  138   67                                                            
CONECT  139   67                                                            
MASTER        0    0    0    0    0    0    0    0  139    0  286    0
END
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3D PDB for NP0011694 (Variapeptin)

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SMILES for NP0011694 (Variapeptin)
[H]ON1C(=O)[C@@]2([H])N(N([H])C([H])([H])C([H])([H])C2([H])[H])C(=O)[C@]([H])(N([H])C(=O)[C@@](O[H])(C([H])([H])[H])[C@@]2(O[H])O[C@@]([H])(C([H])([H])[H])[C@]([H])(C([H])([H])[C@]([H])(C([H])([H])[H])C([H])([H])C([H])([H])[H])C([H])([H])C2([H])[H])[C@@]([H])(OC(=O)[C@@]([H])(N([H])C(=O)[C@@]2([H])N(N([H])C([H])([H])C([H])([H])C2([H])[H])C(=O)[C@]([H])(N(C(=O)[C@@]1([H])C([H])([H])[H])C([H])([H])[H])C([H])([H])C1=C([H])C([H])=C([H])C([H])=C1[H])C([H])([H])O[H])C([H])(C([H])([H])[H])C([H])([H])[H]
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INCHI for NP0011694 (Variapeptin)
InChI=1S/C46H72N8O13/c1-9-27(4)23-31-19-20-46(64,67-29(31)6)45(7,63)44(62)50-36-37(26(2)3)66-43(61)32(25-55)49-38(56)33-17-13-21-47-52(33)40(58)35(24-30-15-11-10-12-16-30)51(8)39(57)28(5)54(65)41(59)34-18-14-22-48-53(34)42(36)60/h10-12,15-16,26-29,31-37,47-48,55,63-65H,9,13-14,17-25H2,1-8H3,(H,49,56)(H,50,62)/t27-,28-,29+,31+,32+,33+,34+,35-,36-,37+,45+,46+/m1/s1
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Synonyms
ValueSource
N-[3-Benzyl-7,22-dihydroxy-20-(hydroxymethyl)-4,6-dimethyl-2,5,8,15,19-pentaoxo-17-(propan-2-yl)-18-oxa-1,4,7,13,14,21,27-heptaazatricyclo[21.4.0.0,]heptacos-21-en-16-yl]-2-hydroxy-2-[2-hydroxy-6-methyl-5-(2-methylbutyl)oxan-2-yl]propanimidateGenerator
Chemical FormulaC46H72N8O13
Average Mass945.1250 Da
Monoisotopic Mass944.52188 Da
IUPAC Name(2R)-N-[(3R,6R,9S,17S,20S,23S)-3-benzyl-7-hydroxy-20-(hydroxymethyl)-4,6-dimethyl-2,5,8,15,19,22-hexaoxo-17-(propan-2-yl)-18-oxa-1,4,7,13,14,21,27-heptaazatricyclo[21.4.0.0^{9,14}]heptacosan-16-yl]-2-hydroxy-2-[(2S,5S,6S)-2-hydroxy-6-methyl-5-[(2R)-2-methylbutyl]oxan-2-yl]propanamide
Traditional Name(2R)-N-[(3R,6R,9S,17S,20S,23S)-3-benzyl-7-hydroxy-20-(hydroxymethyl)-17-isopropyl-4,6-dimethyl-2,5,8,15,19,22-hexaoxo-18-oxa-1,4,7,13,14,21,27-heptaazatricyclo[21.4.0.0^{9,14}]heptacosan-16-yl]-2-hydroxy-2-[(2S,5S,6S)-2-hydroxy-6-methyl-5-[(2R)-2-methylbutyl]oxan-2-yl]propanamide
CAS Registry NumberNot Available
SMILES
CCC(C)CC1CCC(O)(OC1C)C(C)(O)C(=O)NC1C(OC(=O)C(CO)NC(=O)C2CCCNN2C(=O)C(CC2=CC=CC=C2)N(C)C(=O)C(C)N(O)C(=O)C2CCCNN2C1=O)C(C)C
InChI Identifier
InChI=1S/C46H72N8O13/c1-9-27(4)23-31-19-20-46(64,67-29(31)6)45(7,63)44(62)50-36-37(26(2)3)66-43(61)32(25-55)49-38(56)33-17-13-21-47-52(33)40(58)35(24-30-15-11-10-12-16-30)51(8)39(57)28(5)54(65)41(59)34-18-14-22-48-53(34)42(36)60/h10-12,15-16,26-29,31-37,47-48,55,63-65H,9,13-14,17-25H2,1-8H3,(H,49,56)(H,50,62)
InChI KeyPBXKWAYVRNEWSB-UHFFFAOYSA-N
Experimental Spectra
Not Available
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 25 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 252 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 50 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 75 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 101 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 126 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 151 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 176 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 201 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 226 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Streptomyces variabilisNPAtlas
Chemical Taxonomy
Description Belongs to the class of organic compounds known as cyclic depsipeptides. These are natural or synthetic compounds having sequences of amino and hydroxy carboxylic acid residues (usually α-amino and α-hydroxy acids) connected in a ring. The residues are commonly but not necessarily regularly alternating.
KingdomOrganic compounds  
Super ClassOrganic acids and derivatives  
ClassPeptidomimetics  
Sub ClassDepsipeptides  
Direct ParentCyclic depsipeptides  
Alternative Parents
Substituents
  • Cyclic depsipeptide
    • 

  • Macrolide lactam
    • 

  • Alpha-amino acid ester
    • 

  • Macrolactam
    • 

  • N-acyl-alpha amino acid or derivatives
    • 

  • Alpha-amino acid or derivatives
    • 

  • Monocyclic benzene moiety
    • 

  • 1,2-diazinane
    • 

  • Benzenoid
    • 

  • Oxane
    • 

  • Tertiary carboxylic acid amide
    • 

  • Tertiary alcohol
    • 

  • Carboxamide group
    • 

  • Carboxylic acid ester
    • 

  • Carboxylic acid hydrazide
    • 

  • Hemiacetal
    • 

  • Hydroxamic acid
    • 

  • Lactam
    • 

  • Lactone
    • 

  • Secondary carboxylic acid amide
    • 

  • Oxacycle
    • 

  • Azacycle
    • 

  • Monocarboxylic acid or derivatives
    • 

  • Organoheterocyclic compound
    • 

  • Carboxylic acid derivative
    • 

  • Alcohol
    • 

  • Carbonyl group
    • 

  • Organopnictogen compound
    • 

  • Hydrocarbon derivative
    • 

  • Organic oxide
    • 

  • Organic oxygen compound
    • 

  • Organic nitrogen compound
    • 

  • Organonitrogen compound
    • 

  • Organooxygen compound
    • 

  • Primary alcohol
    • 

  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP1.44ALOGPS
logP0.94ChemAxon
logS-3.9ALOGPS
pKa (Strongest Acidic)7.67ChemAxon
pKa (Strongest Basic)4.33ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area279.95 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity261.76 m³·mol⁻¹ChemAxon
Polarizability99.23 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA016175  
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2339289  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3081754  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Nakagawa M, Hayakawa Y, Furihata K, Seto H: Structural studies on new depsipeptide antibiotics, variapeptin and citropeptin. J Antibiot (Tokyo). 1990 May;43(5):477-84. doi: 10.7164/antibiotics.43.477. [PubMed:2358400  ]