NP-MRD: Showing NP-Card for Amipurimycin (NP0021672)

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Record Information

Version

1.0

Created at

2021-01-06 06:57:01 UTC

Updated at

2021-07-15 17:36:58 UTC

NP-MRD ID

NP0021672

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Amipurimycin

Provided By

NPAtlas

Description

Amipurimycin is found in Streptomyces and Streptomyces novoguineensis. It was first documented in 1977 (PMID: 557031). Based on a literature review a significant number of articles have been published on Amipurimycin (PMID: 33835677) (PMID: 31190371) (PMID: 31150226) (PMID: 30990701) (PMID: 29356246) (PMID: 27559421).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242105173D          

 64 67  0  0  0  0            999 V2000
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M  END

     RDKit          3D

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M  END


  Mrv1652306242105173D          

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    3.8988    0.0413    0.9490 C   0  0  1  0  0  0  0  0  0  0  0  0
    5.1670    0.5973    1.6076 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.1995    1.9880    1.0476 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7672    1.8063   -0.3964 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1106    3.0064   -0.8097 N   0  0  1  0  0  0  0  0  0  0  0  0
    0.2063   -0.8230   -2.9370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1535   -1.5470   -3.3461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9653   -0.7830   -3.6381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5087   -1.8496   -0.3178 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.6794   -2.2595    0.5423 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7201   -2.6319   -0.3041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2882   -3.5356    1.2949 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3990   -3.9798    2.0001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8368   -4.6300    0.3591 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8169   -4.9915   -0.5519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1063   -1.2386    1.5379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5241   -1.1999    1.4848 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8642    2.0492    0.3929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1525    2.4376   -0.7069 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1483    4.5643   -2.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3447    3.7020   -3.5275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4201    4.1970    0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8308    0.4674    3.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0533    0.4106    2.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503   -0.3463   -1.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1812    1.0757   -2.0041 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8956   -1.1677   -0.8459 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4403   -0.1836   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0451    0.4860    1.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9421   -1.0556    0.9953 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0288    0.0149    1.2343 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0484    0.5835    2.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2118    2.4434    1.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4522    2.6138    1.5853 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7292    1.6785   -0.9731 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6455    3.4800    0.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8306    3.6671   -1.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7087   -1.4655   -3.5742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5094   -2.4982   -1.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3916   -1.9221    0.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3330   -2.8129   -1.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4393   -3.3226    1.9794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1660   -4.3665    2.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0862   -4.3479   -0.1885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5882   -5.5005    0.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5517   -5.4112   -0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9166   -1.6286    2.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8269   -1.1726    0.5318 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  3  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  2  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 12 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 11 25  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  6  0  0  0
 26 28  1  0  0  0  0
 28 29  1  0  0  0  0
 28 30  1  0  0  0  0
 30 31  1  0  0  0  0
 26 32  1  0  0  0  0
 32 33  1  0  0  0  0
  8 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35  2  1  0  0  0  0
 34  5  1  0  0  0  0
 32  9  1  0  0  0  0
 20 16  1  0  0  0  0
  1 36  1  0  0  0  0
  1 37  1  0  0  0  0
  4 38  1  0  0  0  0
  7 39  1  0  0  0  0
  9 40  1  1  0  0  0
 11 41  1  6  0  0  0
 12 42  1  6  0  0  0
 13 43  1  0  0  0  0
 16 44  1  6  0  0  0
 17 45  1  0  0  0  0
 17 46  1  0  0  0  0
 18 47  1  0  0  0  0
 18 48  1  0  0  0  0
 19 49  1  0  0  0  0
 19 50  1  0  0  0  0
 20 51  1  6  0  0  0
 21 52  1  0  0  0  0
 21 53  1  0  0  0  0
 24 54  1  0  0  0  0
 25 55  1  0  0  0  0
 25 56  1  0  0  0  0
 27 57  1  0  0  0  0
 28 58  1  1  0  0  0
 29 59  1  0  0  0  0
 30 60  1  0  0  0  0
 30 61  1  0  0  0  0
 31 62  1  0  0  0  0
 32 63  1  1  0  0  0
 33 64  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0021672

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]([H])(N([H])C(=O)[C@]1([H])C([H])([H])C([H])([H])C([H])([H])[C@]1([H])N([H])[H])[C@]1([H])O[C@@]([H])(N2C([H])=NC3=C([H])N=C(N=C23)N([H])[H])[C@@]([H])(O[H])[C@@](O[H])(C1([H])[H])[C@@]([H])(O[H])C([H])([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C20H29N7O8/c21-9-3-1-2-8(9)16(31)25-13(18(32)33)11-4-20(34,12(29)6-28)14(30)17(35-11)27-7-24-10-5-23-19(22)26-15(10)27/h5,7-9,11-14,17,28-30,34H,1-4,6,21H2,(H,25,31)(H,32,33)(H2,22,23,26)/t8-,9+,11-,12+,13-,14-,17-,20-/m1/s1

> <INCHI_KEY>
BHAUQSKSOITMND-KVKUBTPSSA-N

> <FORMULA>
C20H29N7O8

> <MOLECULAR_WEIGHT>
495.493

> <EXACT_MASS>
495.207760922

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
64

> <JCHEM_AVERAGE_POLARIZABILITY>
47.29455656435351

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-[(2R,4R,5S,6R)-6-(2-amino-9H-purin-9-yl)-4-[(1S)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]-2-{[(1R,2S)-2-aminocyclopentyl]formamido}acetic acid

> <ALOGPS_LOGP>
-2.74

> <JCHEM_LOGP>
-5.874673733125116

> <ALOGPS_LOGS>
-1.87

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.064610083052434

> <JCHEM_PKA_STRONGEST_ACIDIC>
-1.793436975318877

> <JCHEM_PKA_STRONGEST_BASIC>
9.400137782284613

> <JCHEM_POLAR_SURFACE_AREA>
252.18999999999994

> <JCHEM_REFRACTIVITY>
116.54329999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(R)-{[(1R,2S)-2-aminocyclopentyl]formamido}[(2R,4R,5S,6R)-6-(2-aminopurin-9-yl)-4-[(1S)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 64 67  0  0  0  0  0  0  0  0999 V2000
   -1.9797    3.9549   -2.5938 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6264    3.4612   -1.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7867    4.0765   -1.0635 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4979    3.7160    0.0040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0368    2.6753    0.7631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5022    2.0763    1.8762 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6679    1.1056    2.2114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6734    1.0871    1.3130 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5723    0.1308    1.3861 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6335    0.3422    0.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7647   -0.4051   -0.7318 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3192    0.0005   -1.7023 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6411   -0.2159   -1.1550 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6017    0.8174   -1.0245 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2629    1.9678   -1.4100 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9340    0.5706   -0.4669 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8988    0.0413    0.9490 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1670    0.5973    1.6076 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1995    1.9880    1.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672    1.8063   -0.3964 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1106    3.0064   -0.8097 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2063   -0.8230   -2.9370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1535   -1.5470   -3.3461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9653   -0.7830   -3.6381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5087   -1.8496   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6794   -2.2595    0.5423 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7201   -2.6319   -0.3041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2882   -3.5356    1.2949 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3990   -3.9798    2.0001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8368   -4.6300    0.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8169   -4.9915   -0.5519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1063   -1.2386    1.5379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5241   -1.1999    1.4848 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8642    2.0492    0.3929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1525    2.4376   -0.7069 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1483    4.5643   -2.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3447    3.7020   -3.5275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4201    4.1970    0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8308    0.4674    3.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0533    0.4106    2.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503   -0.3463   -1.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1812    1.0757   -2.0041 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8956   -1.1677   -0.8459 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4403   -0.1836   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0451    0.4860    1.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9421   -1.0556    0.9953 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0288    0.0149    1.2343 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0484    0.5835    2.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2118    2.4434    1.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4522    2.6138    1.5853 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7292    1.6785   -0.9731 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6455    3.4800    0.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8306    3.6671   -1.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7087   -1.4655   -3.5742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5094   -2.4982   -1.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3916   -1.9221    0.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3330   -2.8129   -1.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4393   -3.3226    1.9794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1660   -4.3665    2.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0862   -4.3479   -0.1885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5882   -5.5005    0.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5517   -5.4112   -0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9166   -1.6286    2.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8269   -1.1726    0.5318 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 12 22  1  0
 22 23  2  0
 22 24  1  0
 11 25  1  0
 25 26  1  0
 26 27  1  6
 26 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
 26 32  1  0
 32 33  1  0
  8 34  1  0
 34 35  2  0
 35  2  1  0
 34  5  1  0
 32  9  1  0
 20 16  1  0
  1 36  1  0
  1 37  1  0
  4 38  1  0
  7 39  1  0
  9 40  1  1
 11 41  1  6
 12 42  1  6
 13 43  1  0
 16 44  1  6
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  6
 21 52  1  0
 21 53  1  0
 24 54  1  0
 25 55  1  0
 25 56  1  0
 27 57  1  0
 28 58  1  1
 29 59  1  0
 30 60  1  0
 30 61  1  0
 31 62  1  0
 32 63  1  1
 33 64  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  N   UNK     0      -1.980   3.955  -2.594  0.00  0.00           N+0
HETATM    2  C   UNK     0      -2.626   3.461  -1.435  0.00  0.00           C+0
HETATM    3  N   UNK     0      -3.787   4.077  -1.063  0.00  0.00           N+0
HETATM    4  C   UNK     0      -4.498   3.716   0.004  0.00  0.00           C+0
HETATM    5  C   UNK     0      -4.037   2.675   0.763  0.00  0.00           C+0
HETATM    6  N   UNK     0      -4.502   2.076   1.876  0.00  0.00           N+0
HETATM    7  C   UNK     0      -3.668   1.106   2.211  0.00  0.00           C+0
HETATM    8  N   UNK     0      -2.673   1.087   1.313  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.572   0.131   1.386  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.634   0.342   0.409  0.00  0.00           O+0
HETATM   11  C   UNK     0      -0.765  -0.405  -0.732  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.319   0.001  -1.702  0.00  0.00           C+0
HETATM   13  N   UNK     0       1.641  -0.216  -1.155  0.00  0.00           N+0
HETATM   14  C   UNK     0       2.602   0.817  -1.024  0.00  0.00           C+0
HETATM   15  O   UNK     0       2.263   1.968  -1.410  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.934   0.571  -0.467  0.00  0.00           C+0
HETATM   17  C   UNK     0       3.899   0.041   0.949  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.167   0.597   1.608  0.00  0.00           C+0
HETATM   19  C   UNK     0       5.199   1.988   1.048  0.00  0.00           C+0
HETATM   20  C   UNK     0       4.767   1.806  -0.396  0.00  0.00           C+0
HETATM   21  N   UNK     0       4.111   3.006  -0.810  0.00  0.00           N+0
HETATM   22  C   UNK     0       0.206  -0.823  -2.937  0.00  0.00           C+0
HETATM   23  O   UNK     0       1.153  -1.547  -3.346  0.00  0.00           O+0
HETATM   24  O   UNK     0      -0.965  -0.783  -3.638  0.00  0.00           O+0
HETATM   25  C   UNK     0      -0.509  -1.850  -0.318  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.679  -2.260   0.542  0.00  0.00           C+0
HETATM   27  O   UNK     0      -2.720  -2.632  -0.304  0.00  0.00           O+0
HETATM   28  C   UNK     0      -1.288  -3.536   1.295  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.399  -3.980   2.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -0.837  -4.630   0.359  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.817  -4.992  -0.552  0.00  0.00           O+0
HETATM   32  C   UNK     0      -2.106  -1.239   1.538  0.00  0.00           C+0
HETATM   33  O   UNK     0      -3.524  -1.200   1.485  0.00  0.00           O+0
HETATM   34  C   UNK     0      -2.864   2.049   0.393  0.00  0.00           C+0
HETATM   35  N   UNK     0      -2.152   2.438  -0.707  0.00  0.00           N+0
HETATM   36  H   UNK     0      -1.148   4.564  -2.526  0.00  0.00           H+0
HETATM   37  H   UNK     0      -2.345   3.702  -3.527  0.00  0.00           H+0
HETATM   38  H   UNK     0      -5.420   4.197   0.308  0.00  0.00           H+0
HETATM   39  H   UNK     0      -3.831   0.467   3.090  0.00  0.00           H+0
HETATM   40  H   UNK     0      -1.053   0.411   2.356  0.00  0.00           H+0
HETATM   41  H   UNK     0      -1.750  -0.346  -1.192  0.00  0.00           H+0
HETATM   42  H   UNK     0       0.181   1.076  -2.004  0.00  0.00           H+0
HETATM   43  H   UNK     0       1.896  -1.168  -0.846  0.00  0.00           H+0
HETATM   44  H   UNK     0       4.440  -0.184  -1.111  0.00  0.00           H+0
HETATM   45  H   UNK     0       3.045   0.486   1.460  0.00  0.00           H+0
HETATM   46  H   UNK     0       3.942  -1.056   0.995  0.00  0.00           H+0
HETATM   47  H   UNK     0       6.029   0.015   1.234  0.00  0.00           H+0
HETATM   48  H   UNK     0       5.048   0.584   2.699  0.00  0.00           H+0
HETATM   49  H   UNK     0       6.212   2.443   1.126  0.00  0.00           H+0
HETATM   50  H   UNK     0       4.452   2.614   1.585  0.00  0.00           H+0
HETATM   51  H   UNK     0       5.729   1.679  -0.973  0.00  0.00           H+0
HETATM   52  H   UNK     0       3.646   3.480   0.020  0.00  0.00           H+0
HETATM   53  H   UNK     0       4.831   3.667  -1.227  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.709  -1.466  -3.574  0.00  0.00           H+0
HETATM   55  H   UNK     0      -0.509  -2.498  -1.212  0.00  0.00           H+0
HETATM   56  H   UNK     0       0.392  -1.922   0.302  0.00  0.00           H+0
HETATM   57  H   UNK     0      -2.333  -2.813  -1.193  0.00  0.00           H+0
HETATM   58  H   UNK     0      -0.439  -3.323   1.979  0.00  0.00           H+0
HETATM   59  H   UNK     0      -2.166  -4.367   2.880  0.00  0.00           H+0
HETATM   60  H   UNK     0       0.086  -4.348  -0.189  0.00  0.00           H+0
HETATM   61  H   UNK     0      -0.588  -5.500   0.984  0.00  0.00           H+0
HETATM   62  H   UNK     0      -2.552  -5.411  -0.035  0.00  0.00           H+0
HETATM   63  H   UNK     0      -1.917  -1.629   2.584  0.00  0.00           H+0
HETATM   64  H   UNK     0      -3.827  -1.173   0.532  0.00  0.00           H+0
CONECT    1    2   36   37                                                  
CONECT    2    1    3   35                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5   38                                                  
CONECT    5    4    6   34                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8   39                                                  
CONECT    8    7    9   34                                                  
CONECT    9    8   10   32   40                                             
CONECT   10    9   11                                                       
CONECT   11   10   12   25   41                                             
CONECT   12   11   13   22   42                                             
CONECT   13   12   14   43                                                  
CONECT   14   13   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   20   44                                             
CONECT   17   16   18   45   46                                             
CONECT   18   17   19   47   48                                             
CONECT   19   18   20   49   50                                             
CONECT   20   19   21   16   51                                             
CONECT   21   20   52   53                                                  
CONECT   22   12   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   54                                                       
CONECT   25   11   26   55   56                                             
CONECT   26   25   27   28   32                                             
CONECT   27   26   57                                                       
CONECT   28   26   29   30   58                                             
CONECT   29   28   59                                                       
CONECT   30   28   31   60   61                                             
CONECT   31   30   62                                                       
CONECT   32   26   33    9   63                                             
CONECT   33   32   64                                                       
CONECT   34    8   35    5                                                  
CONECT   35   34    2                                                       
CONECT   36    1                                                            
CONECT   37    1                                                            
CONECT   38    4                                                            
CONECT   39    7                                                            
CONECT   40    9                                                            
CONECT   41   11                                                            
CONECT   42   12                                                            
CONECT   43   13                                                            
CONECT   44   16                                                            
CONECT   45   17                                                            
CONECT   46   17                                                            
CONECT   47   18                                                            
CONECT   48   18                                                            
CONECT   49   19                                                            
CONECT   50   19                                                            
CONECT   51   20                                                            
CONECT   52   21                                                            
CONECT   53   21                                                            
CONECT   54   24                                                            
CONECT   55   25                                                            
CONECT   56   25                                                            
CONECT   57   27                                                            
CONECT   58   28                                                            
CONECT   59   29                                                            
CONECT   60   30                                                            
CONECT   61   30                                                            
CONECT   62   31                                                            
CONECT   63   32                                                            
CONECT   64   33                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  134    0
END

RDKit          3D

64 67  0  0  0  0  0  0  0  0999 V2000
   -1.9797    3.9549   -2.5938 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6264    3.4612   -1.4348 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7867    4.0765   -1.0635 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4979    3.7160    0.0040 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0368    2.6753    0.7631 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5022    2.0763    1.8762 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6679    1.1056    2.2114 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6734    1.0871    1.3130 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5723    0.1308    1.3861 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6335    0.3422    0.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7647   -0.4051   -0.7318 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3192    0.0005   -1.7023 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6411   -0.2159   -1.1550 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6017    0.8174   -1.0245 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2629    1.9678   -1.4100 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9340    0.5706   -0.4669 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.8988    0.0413    0.9490 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1670    0.5973    1.6076 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1995    1.9880    1.0476 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7672    1.8063   -0.3964 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1106    3.0064   -0.8097 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2063   -0.8230   -2.9370 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1535   -1.5470   -3.3461 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9653   -0.7830   -3.6381 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5087   -1.8496   -0.3178 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6794   -2.2595    0.5423 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.7201   -2.6319   -0.3041 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2882   -3.5356    1.2949 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.3990   -3.9798    2.0001 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8368   -4.6300    0.3591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8169   -4.9915   -0.5519 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1063   -1.2386    1.5379 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5241   -1.1999    1.4848 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8642    2.0492    0.3929 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1525    2.4376   -0.7069 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1483    4.5643   -2.5257 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3447    3.7020   -3.5275 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4201    4.1970    0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8308    0.4674    3.0898 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0533    0.4106    2.3558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7503   -0.3463   -1.1919 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1812    1.0757   -2.0041 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8956   -1.1677   -0.8459 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4403   -0.1836   -1.1106 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0451    0.4860    1.4595 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9421   -1.0556    0.9953 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0288    0.0149    1.2343 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0484    0.5835    2.6989 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2118    2.4434    1.1261 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4522    2.6138    1.5853 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7292    1.6785   -0.9731 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6455    3.4800    0.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8306    3.6671   -1.2270 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7087   -1.4655   -3.5742 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5094   -2.4982   -1.2122 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3916   -1.9221    0.3019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3330   -2.8129   -1.1926 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4393   -3.3226    1.9794 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1660   -4.3665    2.8799 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0862   -4.3479   -0.1885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5882   -5.5005    0.9843 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5517   -5.4112   -0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9166   -1.6286    2.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8269   -1.1726    0.5318 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  2  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 12 22  1  0
 22 23  2  0
 22 24  1  0
 11 25  1  0
 25 26  1  0
 26 27  1  6
 26 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
 26 32  1  0
 32 33  1  0
  8 34  1  0
 34 35  2  0
 35  2  1  0
 34  5  1  0
 32  9  1  0
 20 16  1  0
  1 36  1  0
  1 37  1  0
  4 38  1  0
  7 39  1  0
  9 40  1  1
 11 41  1  6
 12 42  1  6
 13 43  1  0
 16 44  1  6
 17 45  1  0
 17 46  1  0
 18 47  1  0
 18 48  1  0
 19 49  1  0
 19 50  1  0
 20 51  1  6
 21 52  1  0
 21 53  1  0
 24 54  1  0
 25 55  1  0
 25 56  1  0
 27 57  1  0
 28 58  1  1
 29 59  1  0
 30 60  1  0
 30 61  1  0
 31 62  1  0
 32 63  1  1
 33 64  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(2R)-2-({[(1R,2S)-2-aminocyclopentyl](hydroxy)methylidene}amino)-2-[(2R,4R,5S,6R)-4-[(1S)-1,2-dihydroxyethyl]-4,5-dihydroxy-6-(2-imino-2,9-dihydro-1H-purin-9-yl)oxan-2-yl]acetate	Generator

Chemical Formula

C₂₀H₂₉N₇O₈

Average Mass

495.4930 Da

Monoisotopic Mass

495.20776 Da

IUPAC Name

(2R)-2-[(2R,4R,5S,6R)-6-(2-amino-9H-purin-9-yl)-4-[(1S)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]-2-{[(1R,2S)-2-aminocyclopentyl]formamido}acetic acid

Traditional Name

(R)-{[(1R,2S)-2-aminocyclopentyl]formamido}[(2R,4R,5S,6R)-6-(2-aminopurin-9-yl)-4-[(1S)-1,2-dihydroxyethyl]-4,5-dihydroxyoxan-2-yl]acetic acid

CAS Registry Number

Not Available

SMILES

N[C@H]1CCC[C@H]1C(=O)N[C@H]([C@H]1C[C@@](O)([C@@H](O)CO)[C@H](O)[C@@H](O1)N1C=NC2=CN=C(N)N=C12)C(O)=O

InChI Identifier

InChI=1S/C20H29N7O8/c21-9-3-1-2-8(9)16(31)25-13(18(32)33)11-4-20(34,12(29)6-28)14(30)17(35-11)27-7-24-10-5-23-19(22)26-15(10)27/h5,7-9,11-14,17,28-30,34H,1-4,6,21H2,(H,25,31)(H,32,33)(H2,22,23,26)/t8-,9+,11-,12+,13-,14-,17-,20-/m1/s1

InChI Key

BHAUQSKSOITMND-KVKUBTPSSA-N

Experimental Spectra

Not Available

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces	NPAtlas	557031
Streptomyces novoguineensis	LOTUS Database	35616633

Species Where Detected

Species Name	Source	Reference
Streptomyces novoguineensis sp. nov. T-36496	KNApSAcK Database	22123792

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	-2.7	ALOGPS
logP	-5.9	ChemAxon
logS	-1.9	ALOGPS
pKa (Strongest Acidic)	-1.8	ChemAxon
pKa (Strongest Basic)	9.4	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	252.19 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	116.54 m³·mol⁻¹	ChemAxon
Polarizability	47.29 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

External Links

NPAtlas ID

NPA021133

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00018118

Chemspider ID

78443143

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139589160

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Iwasa T, Kishi T, Matsuura K, Wakae O: Streptomyces novoguineensis sp. Nov., an amipurimycin producer, and antimicrobial activity of amipurimycin. J Antibiot (Tokyo). 1977 Jan;30(1):1-10. doi: 10.7164/antibiotics.30.1. [PubMed:557031 ]
Yu B, Wang S: Solving the Structural Puzzles of Amipurimycin and Miharamycins Enabled by Stereodivergent Total Synthesis. Chem Rec. 2021 Apr 9. doi: 10.1002/tcr.202100057. [PubMed:33835677 ]
Wang S, Zhang Q, Zhao Y, Sun J, Kang W, Wang F, Pan H, Tang G, Yu B: The Miharamycins and Amipurimycin: their Structural Revision and the Total Synthesis of the Latter. Angew Chem Int Ed Engl. 2019 Jul 29;58(31):10558-10562. doi: 10.1002/anie.201905723. Epub 2019 Jul 1. [PubMed:31190371 ]
Romo AJ, Shiraishi T, Ikeuchi H, Lin GM, Geng Y, Lee YH, Liem PH, Ma T, Ogasawara Y, Shin-Ya K, Nishiyama M, Kuzuyama T, Liu HW: The Amipurimycin and Miharamycin Biosynthetic Gene Clusters: Unraveling the Origins of 2-Aminopurinyl Peptidyl Nucleoside Antibiotics. J Am Chem Soc. 2019 Sep 11;141(36):14152-14159. doi: 10.1021/jacs.9b03021. Epub 2019 Sep 3. [PubMed:31150226 ]
Kang WJ, Pan HX, Wang S, Yu B, Hua H, Tang GL: Identification of the Amipurimycin Gene Cluster Yields Insight into the Biosynthesis of C9 Sugar Nucleoside Antibiotics. Org Lett. 2019 May 3;21(9):3148-3152. doi: 10.1021/acs.orglett.9b00840. Epub 2019 Apr 16. [PubMed:30990701 ]
Wang S, Sun J, Zhang Q, Cao X, Zhao Y, Tang G, Yu B: Amipurimycin: Total Synthesis of the Proposed Structures and Diastereoisomers. Angew Chem Int Ed Engl. 2018 Mar 5;57(11):2884-2888. doi: 10.1002/anie.201800169. Epub 2018 Feb 12. [PubMed:29356246 ]
Markad PR, Kumbhar N, Dhavale DD: Synthesis of the C8'-epimeric thymine pyranosyl amino acid core of amipurimycin. Beilstein J Org Chem. 2016 Aug 5;12:1765-71. doi: 10.3762/bjoc.12.165. eCollection 2016. [PubMed:27559421 ]
Mane RS, Ghosh S, Chopade BA, Reiser O, Dhavale DD: Synthesis of an adenine nucleoside containing the (8'R) epimeric carbohydrate core of amipurimycin and its biological study. J Org Chem. 2011 Apr 15;76(8):2892-5. doi: 10.1021/jo102193q. Epub 2011 Mar 17. [PubMed:21381774 ]
Stauffer CS, Datta A: Synthetic studies on amipurimycin: total synthesis of a thymine nucleoside analogue. J Org Chem. 2008 Jun 6;73(11):4166-74. doi: 10.1021/jo8004815. Epub 2008 May 9. [PubMed:18465899 ]

Showing NP-Card for Amipurimycin (NP0021672)

MOL for NP0021672 (Amipurimycin)

3D MOL for NP0021672 (Amipurimycin)

3D SDF for NP0021672 (Amipurimycin)

3D-SDF for NP0021672 (Amipurimycin)

PDB for NP0021672 (Amipurimycin)

3D PDB for NP0021672 (Amipurimycin)

SMILES for NP0021672 (Amipurimycin)

INCHI for NP0021672 (Amipurimycin)

Structure for NP0021672 (Amipurimycin)

3D Structure for NP0021672 (Amipurimycin)