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Showing NP-Card for A-53930A (NP0023804)

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Record Information
Version2.0
Created at2021-01-06 08:50:55 UTC
Updated at2021-07-15 17:42:44 UTC
NP-MRD IDNP0023804
Secondary Accession NumbersNone
Natural Product Identification
Common NameA-53930A
Provided ByNPAtlasNPAtlas Logo
DescriptionA-53930A is also known as racemomycin. A-53930A is found in Streptomyces, Streptomyces vinaceusdrappus and Streptomyces vinaceusdrappus SANK 62394. A-53930A was first documented in 1998 (PMID: 9727385). Based on a literature review very few articles have been published on A-53930A.
Structure
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MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0023804 (A-53930A)


  Mrv1652307042108213D          

132134  0  0  0  0            999 V2000
   16.5196   -1.5716    1.2661 N   0  0  2  0  0  0  0  0  0  0  0  0
   15.0704   -1.6954    1.0517 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6731   -0.8694   -0.1779 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.0701    0.5812    0.0442 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.7387    1.4639   -1.0895 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.1528    2.8573   -0.8167 N   0  0  2  0  0  0  0  0  0  0  0  0
   13.3515    1.4490   -1.6336 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.3612    1.8541   -0.6263 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5570    1.7130    0.5857 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1388    2.4400   -1.0835 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1304    2.8670   -0.1624 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.5210    1.7306    0.6165 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.4981    2.3132    1.5895 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.8059    1.1920    2.3138 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7521    0.3916    3.0078 N   0  0  2  0  0  0  0  0  0  0  0  0
    6.8621    0.4479    1.3881 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8503    1.4221    0.9435 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6568    2.5113    1.5379 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0038    1.1893   -0.2285 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0545    2.2112   -0.5880 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2341    1.9644   -1.7747 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -1.2262   -1.1951   -1.6706 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for NP0023804 (A-53930A)

     RDKit          3D

132134  0  0  0  0  0  0  0  0999 V2000
   16.5196   -1.5716    1.2661 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.0704   -1.6954    1.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6731   -0.8694   -0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0701    0.5812    0.0442 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0023804 (A-53930A)


  Mrv1652307042108213D          

132134  0  0  0  0            999 V2000
   16.5196   -1.5716    1.2661 N   0  0  2  0  0  0  0  0  0  0  0  0
   15.0704   -1.6954    1.0517 C   0  0  2  0  0  0  0  0  0  0  0  0
   14.6731   -0.8694   -0.1779 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.0701    0.5812    0.0442 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.7387    1.4639   -1.0895 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.1528    2.8573   -0.8167 N   0  0  2  0  0  0  0  0  0  0  0  0
   13.3515    1.4490   -1.6336 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.3612    1.8541   -0.6263 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5570    1.7130    0.5857 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1388    2.4400   -1.0835 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.1304    2.8670   -0.1624 C   0  0  1  0  0  0  0  0  0  0  0  0
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    7.8059    1.1920    2.3138 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7521    0.3916    3.0078 N   0  0  2  0  0  0  0  0  0  0  0  0
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   -2.6764   -3.0550    0.1899 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.6511   -3.7574   -0.6394 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.5260   -3.4117   -2.0714 N   0  0  1  0  0  0  0  0  0  0  0  0
   -5.0654   -3.8827   -0.2884 C   0  0  2  0  0  0  0  0  0  0  0  0
   -5.9022   -2.6802   -0.1701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5285   -1.4862   -0.2668 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3145   -2.8159    0.0793 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2312   -1.7261    0.2138 C   0  0  1  0  0  0  0  0  0  0  0  0
   -9.1351   -1.7063   -1.0079 C   0  0  2  0  0  0  0  0  0  0  0  0
   -9.0561   -0.4438   -1.6973 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4502    0.8042   -1.1417 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4611    1.4659   -1.6449 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6390    2.6605   -0.9133 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.0710    2.9758   -0.5865 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0409    2.6129   -1.2605 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2009    3.7555    0.6125 N   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0131    4.4073    1.1118 C   0  0  2  0  0  0  0  0  0  0  0  0
   -9.8154    3.4766    1.2263 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.6141    4.1205    0.9473 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0709    2.2474    0.4598 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.9109    1.5407   -0.0485 N   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4511   -1.9673   -0.7289 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7167   -2.9759    0.1409 C   0  0  2  0  0  0  0  0  0  0  0  0
  -12.1922   -3.1763    0.3291 C   0  0  1  0  0  0  0  0  0  0  0  0
  -12.8190   -2.0432    0.8044 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0135   -0.8281    0.2376 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6829    0.2739    0.8865 N   0  0  0  0  0  0  0  0  0  0  0  0
  -12.5826   -0.6465   -0.9315 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0577   -2.8163    1.4995 C   0  0  2  0  0  0  0  0  0  0  0  0
  -11.0596   -2.4622    2.4092 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0513   -1.7118    1.4565 C   0  0  1  0  0  0  0  0  0  0  0  0
   -8.3147   -1.6435    2.6401 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9879   -1.9949    0.4364 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.8300   -2.1032    2.1049 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.4804   -1.3817    1.9211 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8826   -2.7558    0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.6045   -0.9993   -0.3531 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.2792   -1.2478   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.5975    0.9194    0.9765 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.1781    0.6110    0.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.4106    1.1825   -1.9656 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.1081    3.0554   -1.1330 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8902    3.1641    0.1255 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1255    0.4109   -2.0059 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2422    2.1082   -2.5313 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9614    2.5707   -2.1043 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6392    3.5867    0.5461 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3492    3.4787   -0.6779 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3117    1.2236    1.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0492    0.9846   -0.0436 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8036    2.9779    1.0647 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0407    2.8976    2.3831 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1796    1.7131    3.1069 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3663   -0.1513    2.3862 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3538   -0.1483    3.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3532   -0.3453    1.9753 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3533    0.0347    0.4975 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1892    0.3119   -0.7207 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6285    3.1813   -0.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3997    2.4397    0.3109 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7052    2.9519   -2.0758 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8975    1.8150   -2.7022 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7711    0.9375   -2.8670 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3225    1.2870   -1.1606 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2791   -0.8440   -2.2130 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4434   -0.3487    0.5908 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9111   -1.8697   -0.1161 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0255   -1.1742   -2.9658 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4896   -2.3496   -1.6525 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.4516    0.2672   -0.8569 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0023804

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@@]1([H])C([H])([H])N([H])C(=O)[C@]2([H])N=C(N([H])[C@]3([H])O[C@]([H])(C([H])([H])OC(=O)N([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]3([H])N([H])C(=O)C([H])([H])[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C([H])([H])[C@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C([H])([H])[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C([H])([H])[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])[H])N([H])[C@@]12[H]

> <INCHI_IDENTIFIER>
InChI=1S/C37H70N14O11/c38-9-1-5-19(39)13-25(53)44-10-2-6-20(40)14-26(54)45-11-3-7-21(41)15-27(55)46-12-4-8-22(42)16-28(56)48-31-33(58)32(57)24(18-61-36(43)60)62-35(31)51-37-49-29-23(52)17-47-34(59)30(29)50-37/h19-24,29-33,35,52,57-58H,1-18,38-42H2,(H2,43,60)(H,44,53)(H,45,54)(H,46,55)(H,47,59)(H,48,56)(H2,49,50,51)/t19-,20-,21+,22-,23-,24+,29-,30+,31+,32-,33-,35+/m0/s1

> <INCHI_KEY>
JFQUFGDPMVGHMW-ISKHFNJQSA-N

> <FORMULA>
C37H70N14O11

> <MOLECULAR_WEIGHT>
887.054

> <EXACT_MASS>
886.53484913

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
132

> <JCHEM_AVERAGE_POLARIZABILITY>
93.49153905032438

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
16

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R,3R,4S,5R,6R)-6-{[(3aR,7S,7aR)-7-hydroxy-4-oxo-1H,3aH,4H,5H,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-5-[(3S)-3-amino-6-[(3R)-3-amino-6-[(3S)-3-amino-6-[(3S)-3,6-diaminohexanamido]hexanamido]hexanamido]hexanamido]-3,4-dihydroxyoxan-2-yl]methyl carbamate

> <ALOGPS_LOGP>
-2.06

> <JCHEM_LOGP>
-8.790812259333332

> <ALOGPS_LOGS>
-3.18

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
6

> <JCHEM_PKA>
12.773303569349416

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.224673993839076

> <JCHEM_PKA_STRONGEST_BASIC>
10.347499854403525

> <JCHEM_POLAR_SURFACE_AREA>
434.26

> <JCHEM_REFRACTIVITY>
219.81270000000004

> <JCHEM_ROTATABLE_BOND_COUNT>
28

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
5.82e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3R,4S,5R,6R)-6-{[(3aR,7S,7aR)-7-hydroxy-4-oxo-1H,3aH,5H,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-5-[(3S)-3-amino-6-[(3R)-3-amino-6-[(3S)-3-amino-6-[(3S)-3,6-diaminohexanamido]hexanamido]hexanamido]hexanamido]-3,4-dihydroxyoxan-2-yl]methyl carbamate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0023804 (A-53930A)

     RDKit          3D

132134  0  0  0  0  0  0  0  0999 V2000
   16.5196   -1.5716    1.2661 N   0  0  0  0  0  0  0  0  0  0  0  0
   15.0704   -1.6954    1.0517 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6731   -0.8694   -0.1779 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0701    0.5812    0.0442 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7387    1.4639   -1.0895 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0023804 (A-53930A)

HEADER    PROTEIN                                 04-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUL-21         0                                  
HETATM    1  N   UNK     0      16.520  -1.572   1.266  0.00  0.00           N+0
HETATM    2  C   UNK     0      15.070  -1.695   1.052  0.00  0.00           C+0
HETATM    3  C   UNK     0      14.673  -0.869  -0.178  0.00  0.00           C+0
HETATM    4  C   UNK     0      15.070   0.581   0.044  0.00  0.00           C+0
HETATM    5  C   UNK     0      14.739   1.464  -1.089  0.00  0.00           C+0
HETATM    6  N   UNK     0      15.153   2.857  -0.817  0.00  0.00           N+0
HETATM    7  C   UNK     0      13.351   1.449  -1.634  0.00  0.00           C+0
HETATM    8  C   UNK     0      12.361   1.854  -0.626  0.00  0.00           C+0
HETATM    9  O   UNK     0      12.557   1.713   0.586  0.00  0.00           O+0
HETATM   10  N   UNK     0      11.139   2.440  -1.083  0.00  0.00           N+0
HETATM   11  C   UNK     0      10.130   2.867  -0.162  0.00  0.00           C+0
HETATM   12  C   UNK     0       9.521   1.731   0.617  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.498   2.313   1.589  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.806   1.192   2.314  0.00  0.00           C+0
HETATM   15  N   UNK     0       8.752   0.392   3.008  0.00  0.00           N+0
HETATM   16  C   UNK     0       6.862   0.448   1.388  0.00  0.00           C+0
HETATM   17  C   UNK     0       5.850   1.422   0.944  0.00  0.00           C+0
HETATM   18  O   UNK     0       5.657   2.511   1.538  0.00  0.00           O+0
HETATM   19  N   UNK     0       5.004   1.189  -0.229  0.00  0.00           N+0
HETATM   20  C   UNK     0       4.054   2.211  -0.588  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.234   1.964  -1.775  0.00  0.00           C+0
HETATM   22  C   UNK     0       2.212   0.939  -1.788  0.00  0.00           C+0
HETATM   23  C   UNK     0       2.475  -0.474  -1.495  0.00  0.00           C+0
HETATM   24  N   UNK     0       2.925  -0.809  -0.192  0.00  0.00           N+0
HETATM   25  C   UNK     0       1.238  -1.279  -1.875  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.029  -0.877  -1.126  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.110  -0.263  -0.038  0.00  0.00           O+0
HETATM   28  N   UNK     0      -1.226  -1.195  -1.671  0.00  0.00           N+0
HETATM   29  C   UNK     0      -2.460  -0.850  -1.020  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.630  -1.581   0.271  0.00  0.00           C+0
HETATM   31  C   UNK     0      -2.676  -3.055   0.190  0.00  0.00           C+0
HETATM   32  C   UNK     0      -3.651  -3.757  -0.639  0.00  0.00           C+0
HETATM   33  N   UNK     0      -3.526  -3.412  -2.071  0.00  0.00           N+0
HETATM   34  C   UNK     0      -5.065  -3.883  -0.288  0.00  0.00           C+0
HETATM   35  C   UNK     0      -5.902  -2.680  -0.170  0.00  0.00           C+0
HETATM   36  O   UNK     0      -5.529  -1.486  -0.267  0.00  0.00           O+0
HETATM   37  N   UNK     0      -7.314  -2.816   0.079  0.00  0.00           N+0
HETATM   38  C   UNK     0      -8.231  -1.726   0.214  0.00  0.00           C+0
HETATM   39  C   UNK     0      -9.135  -1.706  -1.008  0.00  0.00           C+0
HETATM   40  N   UNK     0      -9.056  -0.444  -1.697  0.00  0.00           N+0
HETATM   41  C   UNK     0      -9.450   0.804  -1.142  0.00  0.00           C+0
HETATM   42  N   UNK     0     -10.461   1.466  -1.645  0.00  0.00           N+0
HETATM   43  C   UNK     0     -10.639   2.660  -0.913  0.00  0.00           C+0
HETATM   44  C   UNK     0     -12.071   2.976  -0.587  0.00  0.00           C+0
HETATM   45  O   UNK     0     -13.041   2.613  -1.260  0.00  0.00           O+0
HETATM   46  N   UNK     0     -12.201   3.756   0.613  0.00  0.00           N+0
HETATM   47  C   UNK     0     -11.013   4.407   1.112  0.00  0.00           C+0
HETATM   48  C   UNK     0      -9.815   3.477   1.226  0.00  0.00           C+0
HETATM   49  O   UNK     0      -8.614   4.120   0.947  0.00  0.00           O+0
HETATM   50  C   UNK     0     -10.071   2.247   0.460  0.00  0.00           C+0
HETATM   51  N   UNK     0      -8.911   1.541  -0.049  0.00  0.00           N+0
HETATM   52  O   UNK     0     -10.451  -1.967  -0.729  0.00  0.00           O+0
HETATM   53  C   UNK     0     -10.717  -2.976   0.141  0.00  0.00           C+0
HETATM   54  C   UNK     0     -12.192  -3.176   0.329  0.00  0.00           C+0
HETATM   55  O   UNK     0     -12.819  -2.043   0.804  0.00  0.00           O+0
HETATM   56  C   UNK     0     -13.014  -0.828   0.238  0.00  0.00           C+0
HETATM   57  N   UNK     0     -13.683   0.274   0.887  0.00  0.00           N+0
HETATM   58  O   UNK     0     -12.583  -0.647  -0.932  0.00  0.00           O+0
HETATM   59  C   UNK     0     -10.058  -2.816   1.500  0.00  0.00           C+0
HETATM   60  O   UNK     0     -11.060  -2.462   2.409  0.00  0.00           O+0
HETATM   61  C   UNK     0      -9.051  -1.712   1.456  0.00  0.00           C+0
HETATM   62  O   UNK     0      -8.315  -1.644   2.640  0.00  0.00           O+0
HETATM   63  H   UNK     0      16.988  -1.995   0.436  0.00  0.00           H+0
HETATM   64  H   UNK     0      16.830  -2.103   2.105  0.00  0.00           H+0
HETATM   65  H   UNK     0      14.480  -1.382   1.921  0.00  0.00           H+0
HETATM   66  H   UNK     0      14.883  -2.756   0.787  0.00  0.00           H+0
HETATM   67  H   UNK     0      13.604  -0.999  -0.353  0.00  0.00           H+0
HETATM   68  H   UNK     0      15.279  -1.248  -1.020  0.00  0.00           H+0
HETATM   69  H   UNK     0      14.598   0.919   0.977  0.00  0.00           H+0
HETATM   70  H   UNK     0      16.178   0.611   0.281  0.00  0.00           H+0
HETATM   71  H   UNK     0      15.411   1.183  -1.966  0.00  0.00           H+0
HETATM   72  H   UNK     0      16.108   3.055  -1.133  0.00  0.00           H+0
HETATM   73  H   UNK     0      14.890   3.164   0.126  0.00  0.00           H+0
HETATM   74  H   UNK     0      13.126   0.411  -2.006  0.00  0.00           H+0
HETATM   75  H   UNK     0      13.242   2.108  -2.531  0.00  0.00           H+0
HETATM   76  H   UNK     0      10.961   2.571  -2.104  0.00  0.00           H+0
HETATM   77  H   UNK     0      10.639   3.587   0.546  0.00  0.00           H+0
HETATM   78  H   UNK     0       9.349   3.479  -0.678  0.00  0.00           H+0
HETATM   79  H   UNK     0      10.312   1.224   1.200  0.00  0.00           H+0
HETATM   80  H   UNK     0       9.049   0.985  -0.044  0.00  0.00           H+0
HETATM   81  H   UNK     0       7.804   2.978   1.065  0.00  0.00           H+0
HETATM   82  H   UNK     0       9.041   2.898   2.383  0.00  0.00           H+0
HETATM   83  H   UNK     0       7.180   1.713   3.107  0.00  0.00           H+0
HETATM   84  H   UNK     0       9.366  -0.151   2.386  0.00  0.00           H+0
HETATM   85  H   UNK     0       8.354  -0.148   3.806  0.00  0.00           H+0
HETATM   86  H   UNK     0       6.353  -0.345   1.975  0.00  0.00           H+0
HETATM   87  H   UNK     0       7.353   0.035   0.498  0.00  0.00           H+0
HETATM   88  H   UNK     0       5.189   0.312  -0.721  0.00  0.00           H+0
HETATM   89  H   UNK     0       4.628   3.181  -0.759  0.00  0.00           H+0
HETATM   90  H   UNK     0       3.400   2.440   0.311  0.00  0.00           H+0
HETATM   91  H   UNK     0       2.705   2.952  -2.076  0.00  0.00           H+0
HETATM   92  H   UNK     0       3.898   1.815  -2.702  0.00  0.00           H+0
HETATM   93  H   UNK     0       1.771   0.938  -2.867  0.00  0.00           H+0
HETATM   94  H   UNK     0       1.323   1.287  -1.161  0.00  0.00           H+0
HETATM   95  H   UNK     0       3.279  -0.844  -2.213  0.00  0.00           H+0
HETATM   96  H   UNK     0       2.443  -0.349   0.591  0.00  0.00           H+0
HETATM   97  H   UNK     0       2.911  -1.870  -0.116  0.00  0.00           H+0
HETATM   98  H   UNK     0       1.026  -1.174  -2.966  0.00  0.00           H+0
HETATM   99  H   UNK     0       1.490  -2.350  -1.653  0.00  0.00           H+0
HETATM  100  H   UNK     0      -1.246  -1.720  -2.614  0.00  0.00           H+0
HETATM  101  H   UNK     0      -2.452   0.267  -0.857  0.00  0.00           H+0
HETATM  102  H   UNK     0      -3.287  -1.125  -1.710  0.00  0.00           H+0
HETATM  103  H   UNK     0      -1.626  -1.375   0.829  0.00  0.00           H+0
HETATM  104  H   UNK     0      -3.336  -1.091   0.970  0.00  0.00           H+0
HETATM  105  H   UNK     0      -2.675  -3.471   1.249  0.00  0.00           H+0
HETATM  106  H   UNK     0      -1.640  -3.375  -0.200  0.00  0.00           H+0
HETATM  107  H   UNK     0      -3.263  -4.860  -0.665  0.00  0.00           H+0
HETATM  108  H   UNK     0      -2.736  -3.917  -2.513  0.00  0.00           H+0
HETATM  109  H   UNK     0      -4.391  -3.755  -2.587  0.00  0.00           H+0
HETATM  110  H   UNK     0      -5.243  -4.512   0.635  0.00  0.00           H+0
HETATM  111  H   UNK     0      -5.597  -4.517  -1.082  0.00  0.00           H+0
HETATM  112  H   UNK     0      -7.688  -3.779   0.167  0.00  0.00           H+0
HETATM  113  H   UNK     0      -7.588  -0.796   0.212  0.00  0.00           H+0
HETATM  114  H   UNK     0      -8.761  -2.487  -1.719  0.00  0.00           H+0
HETATM  115  H   UNK     0      -8.681  -0.377  -2.690  0.00  0.00           H+0
HETATM  116  H   UNK     0     -10.109   3.551  -1.281  0.00  0.00           H+0
HETATM  117  H   UNK     0     -13.114   3.847   1.097  0.00  0.00           H+0
HETATM  118  H   UNK     0     -11.244   4.930   2.059  0.00  0.00           H+0
HETATM  119  H   UNK     0     -10.728   5.194   0.364  0.00  0.00           H+0
HETATM  120  H   UNK     0      -9.776   3.198   2.323  0.00  0.00           H+0
HETATM  121  H   UNK     0      -8.663   4.721   0.165  0.00  0.00           H+0
HETATM  122  H   UNK     0     -10.776   1.591   0.972  0.00  0.00           H+0
HETATM  123  H   UNK     0      -7.923   1.518   0.233  0.00  0.00           H+0
HETATM  124  H   UNK     0     -10.335  -3.977  -0.233  0.00  0.00           H+0
HETATM  125  H   UNK     0     -12.600  -3.492  -0.679  0.00  0.00           H+0
HETATM  126  H   UNK     0     -12.407  -4.033   1.023  0.00  0.00           H+0
HETATM  127  H   UNK     0     -14.477   0.707   0.378  0.00  0.00           H+0
HETATM  128  H   UNK     0     -13.359   0.599   1.819  0.00  0.00           H+0
HETATM  129  H   UNK     0      -9.631  -3.765   1.891  0.00  0.00           H+0
HETATM  130  H   UNK     0     -11.289  -3.170   3.026  0.00  0.00           H+0
HETATM  131  H   UNK     0      -9.649  -0.752   1.424  0.00  0.00           H+0
HETATM  132  H   UNK     0      -7.512  -1.086   2.529  0.00  0.00           H+0
CONECT    1    2   63   64                                                  
CONECT    2    1    3   65   66                                             
CONECT    3    2    4   67   68                                             
CONECT    4    3    5   69   70                                             
CONECT    5    4    6    7   71                                             
CONECT    6    5   72   73                                                  
CONECT    7    5    8   74   75                                             
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   76                                                  
CONECT   11   10   12   77   78                                             
CONECT   12   11   13   79   80                                             
CONECT   13   12   14   81   82                                             
CONECT   14   13   15   16   83                                             
CONECT   15   14   84   85                                                  
CONECT   16   14   17   86   87                                             
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20   88                                                  
CONECT   20   19   21   89   90                                             
CONECT   21   20   22   91   92                                             
CONECT   22   21   23   93   94                                             
CONECT   23   22   24   25   95                                             
CONECT   24   23   96   97                                                  
CONECT   25   23   26   98   99                                             
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29  100                                                  
CONECT   29   28   30  101  102                                             
CONECT   30   29   31  103  104                                             
CONECT   31   30   32  105  106                                             
CONECT   32   31   33   34  107                                             
CONECT   33   32  108  109                                                  
CONECT   34   32   35  110  111                                             
CONECT   35   34   36   37                                                  
CONECT   36   35                                                            
CONECT   37   35   38  112                                                  
CONECT   38   37   39   61  113                                             
CONECT   39   38   40   52  114                                             
CONECT   40   39   41  115                                                  
CONECT   41   40   42   51                                                  
CONECT   42   41   43                                                       
CONECT   43   42   44   50  116                                             
CONECT   44   43   45   46                                                  
CONECT   45   44                                                            
CONECT   46   44   47  117                                                  
CONECT   47   46   48  118  119                                             
CONECT   48   47   49   50  120                                             
CONECT   49   48  121                                                       
CONECT   50   48   51   43  122                                             
CONECT   51   50   41  123                                                  
CONECT   52   39   53                                                       
CONECT   53   52   54   59  124                                             
CONECT   54   53   55  125  126                                             
CONECT   55   54   56                                                       
CONECT   56   55   57   58                                                  
CONECT   57   56  127  128                                                  
CONECT   58   56                                                            
CONECT   59   53   60   61  129                                             
CONECT   60   59  130                                                       
CONECT   61   59   62   38  131                                             
CONECT   62   61  132                                                       
CONECT   63    1                                                            
CONECT   64    1                                                            
CONECT   65    2                                                            
CONECT   66    2                                                            
CONECT   67    3                                                            
CONECT   68    3                                                            
CONECT   69    4                                                            
CONECT   70    4                                                            
CONECT   71    5                                                            
CONECT   72    6                                                            
CONECT   73    6                                                            
CONECT   74    7                                                            
CONECT   75    7                                                            
CONECT   76   10                                                            
CONECT   77   11                                                            
CONECT   78   11                                                            
CONECT   79   12                                                            
CONECT   80   12                                                            
CONECT   81   13                                                            
CONECT   82   13                                                            
CONECT   83   14                                                            
CONECT   84   15                                                            
CONECT   85   15                                                            
CONECT   86   16                                                            
CONECT   87   16                                                            
CONECT   88   19                                                            
CONECT   89   20                                                            
CONECT   90   20                                                            
CONECT   91   21                                                            
CONECT   92   21                                                            
CONECT   93   22                                                            
CONECT   94   22                                                            
CONECT   95   23                                                            
CONECT   96   24                                                            
CONECT   97   24                                                            
CONECT   98   25                                                            
CONECT   99   25                                                            
CONECT  100   28                                                            
CONECT  101   29                                                            
CONECT  102   29                                                            
CONECT  103   30                                                            
CONECT  104   30                                                            
CONECT  105   31                                                            
CONECT  106   31                                                            
CONECT  107   32                                                            
CONECT  108   33                                                            
CONECT  109   33                                                            
CONECT  110   34                                                            
CONECT  111   34                                                            
CONECT  112   37                                                            
CONECT  113   38                                                            
CONECT  114   39                                                            
CONECT  115   40                                                            
CONECT  116   43                                                            
CONECT  117   46                                                            
CONECT  118   47                                                            
CONECT  119   47                                                            
CONECT  120   48                                                            
CONECT  121   49                                                            
CONECT  122   50                                                            
CONECT  123   51                                                            
CONECT  124   53                                                            
CONECT  125   54                                                            
CONECT  126   54                                                            
CONECT  127   57                                                            
CONECT  128   57                                                            
CONECT  129   59                                                            
CONECT  130   60                                                            
CONECT  131   61                                                            
CONECT  132   62                                                            
MASTER        0    0    0    0    0    0    0    0  132    0  268    0
END
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3D PDB for NP0023804 (A-53930A)

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SMILES for NP0023804 (A-53930A)
[H]O[C@@]1([H])C([H])([H])N([H])C(=O)[C@]2([H])N=C(N([H])[C@]3([H])O[C@]([H])(C([H])([H])OC(=O)N([H])[H])[C@]([H])(O[H])[C@@]([H])(O[H])[C@@]3([H])N([H])C(=O)C([H])([H])[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C([H])([H])[C@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C([H])([H])[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])C(=O)C([H])([H])[C@@]([H])(N([H])[H])C([H])([H])C([H])([H])C([H])([H])N([H])[H])N([H])[C@@]12[H]
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INCHI for NP0023804 (A-53930A)
InChI=1S/C37H70N14O11/c38-9-1-5-19(39)13-25(53)44-10-2-6-20(40)14-26(54)45-11-3-7-21(41)15-27(55)46-12-4-8-22(42)16-28(56)48-31-33(58)32(57)24(18-61-36(43)60)62-35(31)51-37-49-29-23(52)17-47-34(59)30(29)50-37/h19-24,29-33,35,52,57-58H,1-18,38-42H2,(H2,43,60)(H,44,53)(H,45,54)(H,46,55)(H,47,59)(H,48,56)(H2,49,50,51)/t19-,20-,21+,22-,23-,24+,29-,30+,31+,32-,33-,35+/m0/s1
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View in JSmolView NMR Assignments
Synonyms
ValueSource
RacemomycinMeSH
Racemomycin bMeSH
Racemomycin eMeSH
Racemomycin DMeSH
3,6-Diamino-N-[4-amino-5-({4-amino-5-[(4-amino-5-{[(3R,4S,5R,6R)-2-({4,7-dihydroxy-3H,3ah,6H,7H,7ah-imidazo[4,5-c]pyridin-2-yl}amino)-4,5-dihydroxy-6-[(C-hydroxycarbonimidoyloxy)methyl]oxan-3-yl]-C-hydroxycarbonimidoyl}pentyl)-C-hydroxycarbonimidoyl]pentyl}-C-hydroxycarbonimidoyl)pentyl]hexanimidateGenerator
Chemical FormulaC37H70N14O11
Average Mass887.0540 Da
Monoisotopic Mass886.53485 Da
IUPAC Name[(2R,3R,4S,5R,6R)-6-{[(3aR,7S,7aR)-7-hydroxy-4-oxo-1H,3aH,4H,5H,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-5-[(3S)-3-amino-6-[(3R)-3-amino-6-[(3S)-3-amino-6-[(3S)-3,6-diaminohexanamido]hexanamido]hexanamido]hexanamido]-3,4-dihydroxyoxan-2-yl]methyl carbamate
Traditional Name[(2R,3R,4S,5R,6R)-6-{[(3aR,7S,7aR)-7-hydroxy-4-oxo-1H,3aH,5H,6H,7H,7aH-imidazo[4,5-c]pyridin-2-yl]amino}-5-[(3S)-3-amino-6-[(3R)-3-amino-6-[(3S)-3-amino-6-[(3S)-3,6-diaminohexanamido]hexanamido]hexanamido]hexanamido]-3,4-dihydroxyoxan-2-yl]methyl carbamate
CAS Registry NumberNot Available
SMILES
NCCCC(N)CC(=O)NCCCC(N)CC(=O)NCCCC(N)CC(=O)NCCCC(N)CC(=O)N[C@@H]1[C@H](O)[C@@H](O)[C@@H](COC(N)=O)OC1NC1=NC2C(N1)C(O)CNC2=O
InChI Identifier
InChI=1S/C37H70N14O11/c38-9-1-5-19(39)13-25(53)44-10-2-6-20(40)14-26(54)45-11-3-7-21(41)15-27(55)46-12-4-8-22(42)16-28(56)48-31-33(58)32(57)24(18-61-36(43)60)62-35(31)51-37-49-29-23(52)17-47-34(59)30(29)50-37/h19-24,29-33,35,52,57-58H,1-18,38-42H2,(H2,43,60)(H,44,53)(H,45,54)(H,46,55)(H,47,59)(H,48,56)(H2,49,50,51)/t19?,20?,21?,22?,23?,24-,29?,30?,31-,32+,33+,35?/m1/s1
InChI KeyJFQUFGDPMVGHMW-ISKHFNJQSA-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
StreptomycesNPAtlas
Streptomyces vinaceusdrappusLOTUS Database
Streptomyces vinaceusdrappus SANK 62394Bacteria
Chemical Taxonomy
ClassificationNot classified
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
logP-2.1ALOGPS
logP-8.8ChemAxon
logS-3.2ALOGPS
pKa (Strongest Acidic)12.22ChemAxon
pKa (Strongest Basic)10.35ChemAxon
Physiological Charge6ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area434.26 ŲChemAxon
Rotatable Bond Count28ChemAxon
Refractivity219.81 m³·mol⁻¹ChemAxon
Polarizability93.49 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
NPAtlas IDNPA006266  
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID78445111  
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound139584852  
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References
  1. Hisamoto M, Inaoka Y, Sakaida Y, Kagazaki T, Enokida R, Okazaki T, Haruyama H, Kinoshita T, Matsuda K: A-53930A and B, novel N-type Ca2+ channel blockers. J Antibiot (Tokyo). 1998 Jul;51(7):607-17. doi: 10.7164/antibiotics.51.607. [PubMed:9727385  ]