NP-MRD: Showing NP-Card for Dynemicin A (NP0015941)

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Record Information

Version

2.0

Created at

2021-01-06 01:03:46 UTC

Updated at

2021-07-15 17:21:21 UTC

NP-MRD ID

NP0015941

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Dynemicin A

Provided By

NPAtlas

Description

Dynemicin A is found in Micromonospora, Micromonospora chersina and Micromonospora chersina sp. nov. M956-1. Dynemicin A was first documented in 1989 (PMID: 2793600). Based on a literature review a small amount of articles have been published on Dynemicin A (PMID: 32198800) (PMID: 31976660) (PMID: 30762044) (PMID: 29512267).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117253D          

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  Mrv1652306242117253D          

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   -2.4420   -0.7797    1.3303 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0618    1.1189   -0.6824 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7194    1.7920   -1.6662 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5114    0.9435   -0.5275 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4048    1.4995   -1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0289    2.2480   -2.5095 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7885    1.3276   -1.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2768    0.6130   -0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3735    0.0370    0.6886 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9207   -0.6714    1.7049 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0163    0.2058    0.5353 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0777   -0.3987    1.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5043   -1.0614    2.4608 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9544   -0.2675    3.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6288    1.0258    2.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3105    0.4644    3.5178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1865   -0.5916   -2.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9599    2.0211   -0.2988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7085    1.7054   -2.3611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4578    0.4417   -2.8661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0239    2.1535   -2.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3129   -1.0585    2.7938 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9498   -1.8306    3.7125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7601    2.2450   -1.3359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2434    1.6537   -2.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3851   -3.2793   -3.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2265   -4.5177   -1.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2840   -1.0125    2.3804 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2328    2.5646   -2.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4225    1.7930   -2.0049 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3564    0.4537   -0.0762 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5412   -1.1430    2.4355 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  7  1  0  0  0  0
  4  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
 10 11  1  1  0  0  0
 12 11  1  1  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  1  0  0  0  0
 15 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  1  0  0  0  0
 22 23  3  0  0  0  0
 23 24  1  0  0  0  0
 24 25  2  0  0  0  0
 25 26  1  0  0  0  0
 26 27  3  0  0  0  0
 27 28  1  0  0  0  0
 18 29  1  0  0  0  0
 29 30  2  0  0  0  0
 29 31  1  0  0  0  0
 31 32  2  0  0  0  0
 32 33  1  0  0  0  0
 32 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 36 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 28  3  1  0  0  0  0
 38 31  1  0  0  0  0
 12 10  1  0  0  0  0
 19 13  1  0  0  0  0
 21 10  1  0  0  0  0
 28 12  1  0  0  0  0
 39 17  1  0  0  0  0
  1 41  1  0  0  0  0
  1 42  1  0  0  0  0
  1 43  1  0  0  0  0
  7 44  1  0  0  0  0
  8 45  1  1  0  0  0
  9 46  1  0  0  0  0
  9 47  1  0  0  0  0
  9 48  1  0  0  0  0
 14 49  1  0  0  0  0
 16 50  1  0  0  0  0
 20 51  1  0  0  0  0
 21 52  1  6  0  0  0
 24 53  1  0  0  0  0
 25 54  1  0  0  0  0
 28 55  1  1  0  0  0
 33 56  1  0  0  0  0
 34 57  1  0  0  0  0
 35 58  1  0  0  0  0
 37 59  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0015941

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C1=C(OC([H])([H])[H])[C@@]2([H])C#C\C([H])=C([H])/C#C[C@]3([H])N([H])C4=C5C(=O)C6=C(O[H])C([H])=C([H])C(O[H])=C6C(=O)C5=C(O[H])C([H])=C4[C@]22O[C@@]32[C@@]1([H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C30H19NO9/c1-12-19(28(37)38)27(39-2)13-7-5-3-4-6-8-18-29(12)30(13,40-29)14-11-17(34)22-23(24(14)31-18)26(36)21-16(33)10-9-15(32)20(21)25(22)35/h3-4,9-13,18,31-34H,1-2H3,(H,37,38)/b4-3-/t12-,13+,18-,29-,30+/m0/s1

> <INCHI_KEY>
AFMYMMXSQGUCBK-AKMKHHNQSA-N

> <FORMULA>
C30H19NO9

> <MOLECULAR_WEIGHT>
537.48

> <EXACT_MASS>
537.105981196

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
59

> <JCHEM_AVERAGE_POLARIZABILITY>
52.45600994388673

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,4S,5S,8R,11Z,15S)-21,24,28-trihydroxy-7-methoxy-5-methyl-19,26-dioxo-3-oxa-16-azaheptacyclo[15.12.0.0^{2,4}.0^{2,8}.0^{4,15}.0^{18,27}.0^{20,25}]nonacosa-1(29),6,11,17,20,22,24,27-octaen-9,13-diyne-6-carboxylic acid

> <ALOGPS_LOGP>
3.86

> <JCHEM_LOGP>
4.778705719333333

> <ALOGPS_LOGS>
-4.29

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
8.286678781431277

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.3683178613230633

> <JCHEM_PKA_STRONGEST_BASIC>
-0.27466603364327025

> <JCHEM_POLAR_SURFACE_AREA>
165.92

> <JCHEM_REFRACTIVITY>
144.16589999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.76e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,4S,5S,8R,11Z,15S)-21,24,28-trihydroxy-7-methoxy-5-methyl-19,26-dioxo-3-oxa-16-azaheptacyclo[15.12.0.0^{2,4}.0^{2,8}.0^{4,15}.0^{18,27}.0^{20,25}]nonacosa-1(29),6,11,17,20,22,24,27-octaen-9,13-diyne-6-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 59 65  0  0  0  0  0  0  0  0999 V2000
   -5.1912    0.1296    2.9314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8200   -0.8643    1.9682 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.2573   -0.0154   -0.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4844   -0.5094   -0.7759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1363   -1.4084   -0.2027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9303   -0.0250   -1.9603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    1.0588   -0.7438 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6839    1.2729   -2.2168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0413    1.0283   -0.3161 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8823    1.6998    0.8897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5811    0.3746    0.8118 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1282    0.1420    1.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3356   -0.5894    2.0523 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7180   -0.7862    2.2483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1383   -1.5201    3.3081 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6374   -0.2294    1.3583 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1611    0.5172    0.2826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8130    0.6800    0.1359 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2877    1.4443   -0.9321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0255    1.0243   -1.4359 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8915   -0.3441   -1.8586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8074   -1.4189   -2.1201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7411   -2.8035   -2.3470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2378   -3.4944   -1.2389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7013   -2.6408   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0350   -1.8824    0.4784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4420   -0.7797    1.3303 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0618    1.1189   -0.6824 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7194    1.7920   -1.6662 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5114    0.9435   -0.5275 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4048    1.4995   -1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0289    2.2480   -2.5095 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7885    1.3276   -1.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2768    0.6130   -0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3735    0.0370    0.6886 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9207   -0.6714    1.7049 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0163    0.2058    0.5353 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0777   -0.3987    1.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5043   -1.0614    2.4608 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9544   -0.2675    3.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6288    1.0258    2.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3105    0.4644    3.5178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1865   -0.5916   -2.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9599    2.0211   -0.2988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7085    1.7054   -2.3611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4578    0.4417   -2.8661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0239    2.1535   -2.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3129   -1.0585    2.7938 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9498   -1.8306    3.7125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7601    2.2450   -1.3359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2434    1.6537   -2.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3851   -3.2793   -3.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2265   -4.5177   -1.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2840   -1.0125    2.3804 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2328    2.5646   -2.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4225    1.7930   -2.0049 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3564    0.4537   -0.0762 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5412   -1.1430    2.4355 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  1
 12 11  1  1
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  3  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  3  0
 27 28  1  0
 18 29  1  0
 29 30  2  0
 29 31  1  0
 31 32  2  0
 32 33  1  0
 32 34  1  0
 34 35  2  0
 35 36  1  0
 36 37  1  0
 36 38  2  0
 38 39  1  0
 39 40  2  0
 28  3  1  0
 38 31  1  0
 12 10  1  0
 19 13  1  0
 21 10  1  0
 28 12  1  0
 39 17  1  0
  1 41  1  0
  1 42  1  0
  1 43  1  0
  7 44  1  0
  8 45  1  1
  9 46  1  0
  9 47  1  0
  9 48  1  0
 14 49  1  0
 16 50  1  0
 20 51  1  0
 21 52  1  6
 24 53  1  0
 25 54  1  0
 28 55  1  1
 33 56  1  0
 34 57  1  0
 35 58  1  0
 37 59  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  C   UNK     0      -5.191   0.130   2.931  0.00  0.00           C+0
HETATM    2  O   UNK     0      -4.820  -0.864   1.968  0.00  0.00           O+0
HETATM    3  C   UNK     0      -3.870  -0.536   1.019  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.257  -0.015  -0.139  0.00  0.00           C+0
HETATM    5  C   UNK     0      -5.484  -0.509  -0.776  0.00  0.00           C+0
HETATM    6  O   UNK     0      -6.136  -1.408  -0.203  0.00  0.00           O+0
HETATM    7  O   UNK     0      -5.930  -0.025  -1.960  0.00  0.00           O+0
HETATM    8  C   UNK     0      -3.468   1.059  -0.744  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.684   1.273  -2.217  0.00  0.00           C+0
HETATM   10  C   UNK     0      -2.041   1.028  -0.316  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.882   1.700   0.890  0.00  0.00           O+0
HETATM   12  C   UNK     0      -1.581   0.375   0.812  0.00  0.00           C+0
HETATM   13  C   UNK     0      -0.128   0.142   1.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.336  -0.589   2.052  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.718  -0.786   2.248  0.00  0.00           C+0
HETATM   16  O   UNK     0       2.138  -1.520   3.308  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.637  -0.229   1.358  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.161   0.517   0.283  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.813   0.680   0.136  0.00  0.00           C+0
HETATM   20  N   UNK     0       0.288   1.444  -0.932  0.00  0.00           N+0
HETATM   21  C   UNK     0      -1.026   1.024  -1.436  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.892  -0.344  -1.859  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.807  -1.419  -2.120  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.741  -2.804  -2.347  0.00  0.00           C+0
HETATM   25  C   UNK     0      -1.238  -3.494  -1.239  0.00  0.00           C+0
HETATM   26  C   UNK     0      -1.701  -2.641  -0.236  0.00  0.00           C+0
HETATM   27  C   UNK     0      -2.035  -1.882   0.478  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.442  -0.780   1.330  0.00  0.00           C+0
HETATM   29  C   UNK     0       3.062   1.119  -0.682  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.719   1.792  -1.666  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.511   0.944  -0.528  0.00  0.00           C+0
HETATM   32  C   UNK     0       5.405   1.500  -1.421  0.00  0.00           C+0
HETATM   33  O   UNK     0       5.029   2.248  -2.510  0.00  0.00           O+0
HETATM   34  C   UNK     0       6.789   1.328  -1.265  0.00  0.00           C+0
HETATM   35  C   UNK     0       7.277   0.613  -0.235  0.00  0.00           C+0
HETATM   36  C   UNK     0       6.373   0.037   0.689  0.00  0.00           C+0
HETATM   37  O   UNK     0       6.921  -0.671   1.705  0.00  0.00           O+0
HETATM   38  C   UNK     0       5.016   0.206   0.535  0.00  0.00           C+0
HETATM   39  C   UNK     0       4.078  -0.399   1.505  0.00  0.00           C+0
HETATM   40  O   UNK     0       4.504  -1.061   2.461  0.00  0.00           O+0
HETATM   41  H   UNK     0      -5.954  -0.268   3.624  0.00  0.00           H+0
HETATM   42  H   UNK     0      -5.629   1.026   2.402  0.00  0.00           H+0
HETATM   43  H   UNK     0      -4.311   0.464   3.518  0.00  0.00           H+0
HETATM   44  H   UNK     0      -6.186  -0.592  -2.763  0.00  0.00           H+0
HETATM   45  H   UNK     0      -3.960   2.021  -0.299  0.00  0.00           H+0
HETATM   46  H   UNK     0      -4.708   1.705  -2.361  0.00  0.00           H+0
HETATM   47  H   UNK     0      -3.458   0.442  -2.866  0.00  0.00           H+0
HETATM   48  H   UNK     0      -3.024   2.154  -2.504  0.00  0.00           H+0
HETATM   49  H   UNK     0      -0.313  -1.059   2.794  0.00  0.00           H+0
HETATM   50  H   UNK     0       2.950  -1.831   3.712  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.760   2.245  -1.336  0.00  0.00           H+0
HETATM   52  H   UNK     0      -1.243   1.654  -2.288  0.00  0.00           H+0
HETATM   53  H   UNK     0      -0.385  -3.279  -3.193  0.00  0.00           H+0
HETATM   54  H   UNK     0      -1.226  -4.518  -1.243  0.00  0.00           H+0
HETATM   55  H   UNK     0      -2.284  -1.012   2.380  0.00  0.00           H+0
HETATM   56  H   UNK     0       4.233   2.565  -2.924  0.00  0.00           H+0
HETATM   57  H   UNK     0       7.423   1.793  -2.005  0.00  0.00           H+0
HETATM   58  H   UNK     0       8.356   0.454  -0.076  0.00  0.00           H+0
HETATM   59  H   UNK     0       6.541  -1.143   2.436  0.00  0.00           H+0
CONECT    1    2   41   42   43                                             
CONECT    2    1    3                                                       
CONECT    3    2    4   28                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5   44                                                       
CONECT    8    4    9   10   45                                             
CONECT    9    8   46   47   48                                             
CONECT   10    8   11   12   21                                             
CONECT   11   10   12                                                       
CONECT   12   11   13   10   28                                             
CONECT   13   12   14   19                                                  
CONECT   14   13   15   49                                                  
CONECT   15   14   16   17                                                  
CONECT   16   15   50                                                       
CONECT   17   15   18   39                                                  
CONECT   18   17   19   29                                                  
CONECT   19   18   20   13                                                  
CONECT   20   19   21   51                                                  
CONECT   21   20   22   10   52                                             
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25   53                                                  
CONECT   25   24   26   54                                                  
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27    3   12   55                                             
CONECT   29   18   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   38                                                  
CONECT   32   31   33   34                                                  
CONECT   33   32   56                                                       
CONECT   34   32   35   57                                                  
CONECT   35   34   36   58                                                  
CONECT   36   35   37   38                                                  
CONECT   37   36   59                                                       
CONECT   38   36   39   31                                                  
CONECT   39   38   40   17                                                  
CONECT   40   39                                                            
CONECT   41    1                                                            
CONECT   42    1                                                            
CONECT   43    1                                                            
CONECT   44    7                                                            
CONECT   45    8                                                            
CONECT   46    9                                                            
CONECT   47    9                                                            
CONECT   48    9                                                            
CONECT   49   14                                                            
CONECT   50   16                                                            
CONECT   51   20                                                            
CONECT   52   21                                                            
CONECT   53   24                                                            
CONECT   54   25                                                            
CONECT   55   28                                                            
CONECT   56   33                                                            
CONECT   57   34                                                            
CONECT   58   35                                                            
CONECT   59   37                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  130    0
END

RDKit          3D

59 65  0  0  0  0  0  0  0  0999 V2000
   -5.1912    0.1296    2.9314 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8200   -0.8643    1.9682 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8697   -0.5355    1.0188 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2573   -0.0154   -0.1390 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4844   -0.5094   -0.7759 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1363   -1.4084   -0.2027 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9303   -0.0250   -1.9603 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4680    1.0588   -0.7438 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6839    1.2729   -2.2168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0413    1.0283   -0.3161 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8823    1.6998    0.8897 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5811    0.3746    0.8118 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1282    0.1420    1.0003 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3356   -0.5894    2.0523 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7180   -0.7862    2.2483 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1383   -1.5201    3.3081 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6374   -0.2294    1.3583 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1611    0.5172    0.2826 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8130    0.6800    0.1359 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2877    1.4443   -0.9321 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0255    1.0243   -1.4359 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8915   -0.3441   -1.8586 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8074   -1.4189   -2.1201 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7411   -2.8035   -2.3470 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2378   -3.4944   -1.2389 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7013   -2.6408   -0.2355 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0350   -1.8824    0.4784 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4420   -0.7797    1.3303 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.0618    1.1189   -0.6824 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7194    1.7920   -1.6662 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5114    0.9435   -0.5275 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4048    1.4995   -1.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0289    2.2480   -2.5095 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.7885    1.3276   -1.2652 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2768    0.6130   -0.2354 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3735    0.0370    0.6886 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9207   -0.6714    1.7049 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0163    0.2058    0.5353 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0777   -0.3987    1.5049 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5043   -1.0614    2.4608 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9544   -0.2675    3.6236 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6288    1.0258    2.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3105    0.4644    3.5178 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1865   -0.5916   -2.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9599    2.0211   -0.2988 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7085    1.7054   -2.3611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4578    0.4417   -2.8661 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0239    2.1535   -2.5040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3129   -1.0585    2.7938 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9498   -1.8306    3.7125 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7601    2.2450   -1.3359 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2434    1.6537   -2.2875 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3851   -3.2793   -3.1931 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2265   -4.5177   -1.2432 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2840   -1.0125    2.3804 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2328    2.5646   -2.9236 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4225    1.7930   -2.0049 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3564    0.4537   -0.0762 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5412   -1.1430    2.4355 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  4  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  1
 12 11  1  1
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 15 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  3  0
 23 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  3  0
 27 28  1  0
 18 29  1  0
 29 30  2  0
 29 31  1  0
 31 32  2  0
 32 33  1  0
 32 34  1  0
 34 35  2  0
 35 36  1  0
 36 37  1  0
 36 38  2  0
 38 39  1  0
 39 40  2  0
 28  3  1  0
 38 31  1  0
 12 10  1  0
 19 13  1  0
 21 10  1  0
 28 12  1  0
 39 17  1  0
  1 41  1  0
  1 42  1  0
  1 43  1  0
  7 44  1  0
  8 45  1  1
  9 46  1  0
  9 47  1  0
  9 48  1  0
 14 49  1  0
 16 50  1  0
 20 51  1  0
 21 52  1  6
 24 53  1  0
 25 54  1  0
 28 55  1  1
 33 56  1  0
 34 57  1  0
 35 58  1  0
 37 59  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(2R,4S,5S,8R,15S)-21,24,28-Trihydroxy-7-methoxy-5-methyl-19,26-dioxo-3-oxa-16-azaheptacyclo[15.12.0.0,.0,.0,.0,.0,]nonacosa-1(29),6,11,17,20,22,24,27-octaen-9,13-diyne-6-carboxylate	Generator

Chemical Formula

C₃₀H₁₉NO₉

Average Mass

537.4800 Da

Monoisotopic Mass

537.10598 Da

IUPAC Name

(2R,4S,5S,8R,11Z,15S)-21,24,28-trihydroxy-7-methoxy-5-methyl-19,26-dioxo-3-oxa-16-azaheptacyclo[15.12.0.0^{2,4}.0^{2,8}.0^{4,15}.0^{18,27}.0^{20,25}]nonacosa-1(29),6,11,17,20,22,24,27-octaen-9,13-diyne-6-carboxylic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

COC1=C([C@H](C)[C@@]23O[C@@]22[C@@H]1C#C\C=C/C#C[C@@H]3NC1=C3C(=O)C4=C(O)C=CC(O)=C4C(=O)C3=C(O)C=C21)C(O)=O

InChI Identifier

InChI=1S/C30H19NO9/c1-12-19(28(37)38)27(39-2)13-7-5-3-4-6-8-18-29(12)30(13,40-29)14-11-17(34)22-23(24(14)31-18)26(36)21-16(33)10-9-15(32)20(21)25(22)35/h3-4,9-13,18,31-34H,1-2H3,(H,37,38)/b4-3-/t12-,13+,18-,29-,30+/m0/s1

InChI Key

AFMYMMXSQGUCBK-AKMKHHNQSA-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
Micromonospora	NPAtlas	2793600
Micromonospora chersina	LOTUS Database	35616633
Micromonospora chersina sp. nov. M956-1	Bacteria	KNApSAcK

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	3.86	ALOGPS
logP	4.78	ChemAxon
logS	-4.3	ALOGPS
pKa (Strongest Acidic)	3.37	ChemAxon
pKa (Strongest Basic)	-0.27	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	165.92 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	144.17 m³·mol⁻¹	ChemAxon
Polarizability	52.46 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA000412

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

C00017528

Chemspider ID

8205706

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Dynemicin A

METLIN ID

Not Available

PubChem Compound

10030135

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Konishi M, Ohkuma H, Matsumoto K, Tsuno T, Kamei H, Miyaki T, Oki T, Kawaguchi H, VanDuyne GD, Clardy J: Dynemicin A, a novel antibiotic with the anthraquinone and 1,5-diyn-3-ene subunit. J Antibiot (Tokyo). 1989 Sep;42(9):1449-52. doi: 10.7164/antibiotics.42.1449. [PubMed:2793600 ]
Cohen DR, Townsend CA: C-N-Coupled Metabolites Yield Insights into Dynemicin A Biosynthesis. Chembiochem. 2020 Aug 3;21(15):2137-2142. doi: 10.1002/cbic.202000177. Epub 2020 Apr 29. [PubMed:32198800 ]
Nicolaou KC, Das D, Lu Y, Rout S, Pitsinos EN, Lyssikatos J, Schammel A, Sandoval J, Hammond M, Aujay M, Gavrilyuk J: Total Synthesis and Biological Evaluation of Tiancimycins A and B, Yangpumicin A, and Related Anthraquinone-Fused Enediyne Antitumor Antibiotics. J Am Chem Soc. 2020 Feb 5;142(5):2549-2561. doi: 10.1021/jacs.9b12522. Epub 2020 Jan 24. [PubMed:31976660 ]
Lang J, Brabec J, Saitow M, Pittner J, Neese F, Demel O: Perturbative triples correction to domain-based local pair natural orbital variants of Mukherjee's state specific coupled cluster method. Phys Chem Chem Phys. 2019 Feb 27;21(9):5022-5038. doi: 10.1039/c8cp03577f. [PubMed:30762044 ]
Cohen DR, Townsend CA: Characterization of an Anthracene Intermediate in Dynemicin Biosynthesis. Angew Chem Int Ed Engl. 2018 May 14;57(20):5650-5654. doi: 10.1002/anie.201802036. Epub 2018 Mar 24. [PubMed:29512267 ]

Showing NP-Card for Dynemicin A (NP0015941)

MOL for NP0015941 (Dynemicin A)

3D MOL for NP0015941 (Dynemicin A)

3D SDF for NP0015941 (Dynemicin A)

3D-SDF for NP0015941 (Dynemicin A)

PDB for NP0015941 (Dynemicin A)

3D PDB for NP0015941 (Dynemicin A)

SMILES for NP0015941 (Dynemicin A)

INCHI for NP0015941 (Dynemicin A)

Structure for NP0015941 (Dynemicin A)

3D Structure for NP0015941 (Dynemicin A)