NP-MRD: Showing NP-Card for Pradimicin A (NP0011950)

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Record Information

Version

1.0

Created at

2021-01-05 21:28:41 UTC

Updated at

2021-07-15 17:10:25 UTC

NP-MRD ID

NP0011950

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pradimicin A

Provided By

NPAtlas

Description

Pradimicin A is found in Actinomadura hibisca. It was first documented in 1990 (PMID: 2387769). Based on a literature review a significant number of articles have been published on pradimicin A (PMID: 2167304) (PMID: 17050611) (PMID: 21598364) (PMID: 21942374).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652307012121573D          

104110  0  0  0  0            999 V2000
    4.5964   -3.1042   -2.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5136   -2.1916   -2.3842 N   0  0  2  0  0  0  0  0  0  0  0  0
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    4.4433   -0.4998   -0.9686 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4045   -1.4021   -0.5625 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6239   -0.8216   -0.2506 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5296   -1.3364   -1.1837 O   0  0  0  0  0  0  0  0  0  0  0  0
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    9.0330   -2.4923    0.2887 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.2520   -2.2823   -0.3504 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

     RDKit          3D

104110  0  0  0  0  0  0  0  0999 V2000
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M  END


  Mrv1652307012121573D          

104110  0  0  0  0            999 V2000
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 60104  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0011950

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]([H])(N([H])C(=O)C1=C(C([H])=C2C(=C1O[H])C1=C(C([H])=C3C(=O)C4=C(O[H])C([H])=C(OC([H])([H])[H])C([H])=C4C(=O)C3=C1O[H])[C@]([H])(O[H])[C@@]2([H])O[C@]1([H])O[C@]([H])(C([H])([H])[H])[C@]([H])(N([H])C([H])([H])[H])[C@]([H])(O[C@]2([H])OC([H])([H])[C@@]([H])(O[H])[C@]([H])(O[H])[C@@]2([H])O[H])[C@@]1([H])O[H])C([H])([H])[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C40H44N2O18/c1-11-6-18-24(31(49)21(11)37(53)42-12(2)38(54)55)23-16(9-17-25(32(23)50)28(46)15-7-14(56-5)8-19(43)22(15)27(17)45)29(47)35(18)59-40-34(52)36(26(41-4)13(3)58-40)60-39-33(51)30(48)20(44)10-57-39/h6-9,12-13,20,26,29-30,33-36,39-41,43-44,47-52H,10H2,1-5H3,(H,42,53)(H,54,55)/t12-,13-,20-,26+,29+,30+,33-,34-,35+,36+,39+,40+/m1/s1

> <INCHI_KEY>
WPICPWIIIBCXCV-NJGWPHBESA-N

> <FORMULA>
C40H44N2O18

> <MOLECULAR_WEIGHT>
840.788

> <EXACT_MASS>
840.258912585

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
104

> <JCHEM_AVERAGE_POLARIZABILITY>
86.3951952061785

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-{[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

> <ALOGPS_LOGP>
0.79

> <JCHEM_LOGP>
-0.5203022662264306

> <ALOGPS_LOGS>
-2.98

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
7.007284610618369

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.736059763766432

> <JCHEM_PKA_STRONGEST_BASIC>
8.99668539326775

> <JCHEM_POLAR_SURFACE_AREA>
320.56

> <JCHEM_REFRACTIVITY>
203.04359999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
8.84e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-{[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

104110  0  0  0  0  0  0  0  0999 V2000
    4.5964   -3.1042   -2.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5136   -2.1916   -2.3842 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8746   -0.7948   -2.3250 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4433   -0.4998   -0.9686 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4045   -1.4021   -0.5625 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6239   -0.8216   -0.2506 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5296   -1.3364   -1.1837 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9763   -2.6047   -0.8170 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0330   -2.4923    0.2887 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.2520   -2.2823   -0.3504 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6735   -1.2000    1.0150 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.2827   -1.0788    2.2392 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1428   -1.1103    1.1135 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.9112   -0.1034    2.0484 O   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9305   -0.3287    1.2890 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.0697    0.3285   -0.1565 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3701    1.0529    0.8111 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6816    1.9001    0.1951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2291    3.0349   -0.4308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1216    3.8501   -1.0793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4960    5.0438   -1.7313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4671    3.5854   -1.1339 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.3726    6.2599   -3.1606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0670    6.3294   -4.6197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5510    7.6024   -2.5558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7855    8.0394   -1.6712 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.7953   -2.9604    2.2823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0882   -3.4149    2.2331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4325   -4.5663    2.8957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7602   -5.0420    2.8513 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0693   -6.2318    3.5471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4655   -5.2453    3.6009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1642   -4.8206    3.6721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1669   -5.4827    4.3744 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8462   -3.6416    2.9841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4984   -3.1084    2.9947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6177   -3.7270    3.6369 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1195    0.1197    1.8242 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0110    0.6412    3.1357 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5854    1.1180   -1.5855 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6713    0.1038   -2.5207 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.3909   -0.6811   -2.6925 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3532   -3.9952   -2.8880 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.6283   -0.6360   -3.1378 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6166    0.2801   -0.3853 H   0  0  0  0  0  0  0  0  0  0  0  0
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    8.4320   -3.1249   -1.6564 H   0  0  0  0  0  0  0  0  0  0  0  0
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   10.5747   -1.3681   -0.2897 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.1504   -2.0034    2.8936 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0
  2  3  1  0
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 33 34  1  0
 33 35  2  0
 35 36  1  0
 36 37  2  0
 37 38  1  0
 38 39  2  0
 39 40  1  0
 40 41  2  0
 41 42  1  0
 40 43  1  0
 43 44  2  0
 43 45  1  0
 45 46  2  0
 46 47  1  0
 47 48  1  0
 48 49  1  0
 47 50  2  0
 50 51  1  0
 51 52  1  0
 51 53  2  0
 53 54  1  0
 54 55  2  0
 37 56  1  0
 56 57  1  0
 17 58  1  0
 58 59  1  0
 59 60  1  0
 59  3  1  0
 13  6  1  0
 56 19  1  0
 35 20  1  0
 41 36  1  0
 53 45  1  0
 54 39  1  0
  1 61  1  0
  1 62  1  0
  1 63  1  0
  2 64  1  0
  3 65  1  6
  4 66  1  6
  6 67  1  6
  8 68  1  0
  8 69  1  0
  9 70  1  1
 10 71  1  0
 11 72  1  6
 12 73  1  0
 13 74  1  1
 14 75  1  0
 15 76  1  1
 16 77  1  0
 17 78  1  1
 19 79  1  1
 21 80  1  0
 23 81  1  0
 23 82  1  0
 23 83  1  0
 27 84  1  0
 28 85  1  6
 29 86  1  0
 29 87  1  0
 29 88  1  0
 32 89  1  0
 34 90  1  0
 38 91  1  0
 42 92  1  0
 46 93  1  0
 49 94  1  0
 49 95  1  0
 49 96  1  0
 50 97  1  0
 52 98  1  0
 56 99  1  1
 57100  1  0
 59101  1  6
 60102  1  0
 60103  1  0
 60104  1  0
M  END

HEADER    PROTEIN                                 01-JUL-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-JUL-21         0                                  
HETATM    1  C   UNK     0       4.596  -3.104  -2.233  0.00  0.00           C+0
HETATM    2  N   UNK     0       3.514  -2.192  -2.384  0.00  0.00           N+0
HETATM    3  C   UNK     0       3.875  -0.795  -2.325  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.443  -0.500  -0.969  0.00  0.00           C+0
HETATM    5  O   UNK     0       5.404  -1.402  -0.563  0.00  0.00           O+0
HETATM    6  C   UNK     0       6.624  -0.822  -0.251  0.00  0.00           C+0
HETATM    7  O   UNK     0       7.530  -1.336  -1.184  0.00  0.00           O+0
HETATM    8  C   UNK     0       7.976  -2.605  -0.817  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.033  -2.492   0.289  0.00  0.00           C+0
HETATM   10  O   UNK     0      10.252  -2.282  -0.350  0.00  0.00           O+0
HETATM   11  C   UNK     0       8.674  -1.200   1.015  0.00  0.00           C+0
HETATM   12  O   UNK     0       9.283  -1.079   2.239  0.00  0.00           O+0
HETATM   13  C   UNK     0       7.143  -1.110   1.113  0.00  0.00           C+0
HETATM   14  O   UNK     0       6.911  -0.103   2.048  0.00  0.00           O+0
HETATM   15  C   UNK     0       3.313  -0.523   0.026  0.00  0.00           C+0
HETATM   16  O   UNK     0       3.930  -0.329   1.289  0.00  0.00           O+0
HETATM   17  C   UNK     0       2.393   0.646  -0.288  0.00  0.00           C+0
HETATM   18  O   UNK     0       1.070   0.329  -0.157  0.00  0.00           O+0
HETATM   19  C   UNK     0       0.370   1.053   0.811  0.00  0.00           C+0
HETATM   20  C   UNK     0      -0.682   1.900   0.195  0.00  0.00           C+0
HETATM   21  C   UNK     0      -0.229   3.035  -0.431  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.122   3.850  -1.079  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.496   5.044  -1.731  0.00  0.00           C+0
HETATM   24  C   UNK     0      -2.467   3.585  -1.134  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.386   4.424  -1.833  0.00  0.00           C+0
HETATM   26  O   UNK     0      -4.628   4.056  -1.861  0.00  0.00           O+0
HETATM   27  N   UNK     0      -3.167   5.617  -2.514  0.00  0.00           N+0
HETATM   28  C   UNK     0      -4.373   6.260  -3.161  0.00  0.00           C+0
HETATM   29  C   UNK     0      -4.067   6.329  -4.620  0.00  0.00           C+0
HETATM   30  C   UNK     0      -4.551   7.602  -2.556  0.00  0.00           C+0
HETATM   31  O   UNK     0      -3.785   8.039  -1.671  0.00  0.00           O+0
HETATM   32  O   UNK     0      -5.596   8.383  -2.989  0.00  0.00           O+0
HETATM   33  C   UNK     0      -2.938   2.409  -0.482  0.00  0.00           C+0
HETATM   34  O   UNK     0      -4.236   2.163  -0.530  0.00  0.00           O+0
HETATM   35  C   UNK     0      -2.049   1.589   0.167  0.00  0.00           C+0
HETATM   36  C   UNK     0      -2.493   0.419   0.940  0.00  0.00           C+0
HETATM   37  C   UNK     0      -1.533  -0.269   1.650  0.00  0.00           C+0
HETATM   38  C   UNK     0      -1.887  -1.420   2.313  0.00  0.00           C+0
HETATM   39  C   UNK     0      -3.179  -1.882   2.274  0.00  0.00           C+0
HETATM   40  C   UNK     0      -4.125  -1.180   1.559  0.00  0.00           C+0
HETATM   41  C   UNK     0      -3.795  -0.005   0.872  0.00  0.00           C+0
HETATM   42  O   UNK     0      -4.797   0.582   0.211  0.00  0.00           O+0
HETATM   43  C   UNK     0      -5.475  -1.722   1.555  0.00  0.00           C+0
HETATM   44  O   UNK     0      -6.398  -1.140   0.925  0.00  0.00           O+0
HETATM   45  C   UNK     0      -5.795  -2.960   2.282  0.00  0.00           C+0
HETATM   46  C   UNK     0      -7.088  -3.415   2.233  0.00  0.00           C+0
HETATM   47  C   UNK     0      -7.433  -4.566   2.896  0.00  0.00           C+0
HETATM   48  O   UNK     0      -8.760  -5.042   2.851  0.00  0.00           O+0
HETATM   49  C   UNK     0      -9.069  -6.232   3.547  0.00  0.00           C+0
HETATM   50  C   UNK     0      -6.465  -5.245   3.601  0.00  0.00           C+0
HETATM   51  C   UNK     0      -5.164  -4.821   3.672  0.00  0.00           C+0
HETATM   52  O   UNK     0      -4.167  -5.483   4.374  0.00  0.00           O+0
HETATM   53  C   UNK     0      -4.846  -3.642   2.984  0.00  0.00           C+0
HETATM   54  C   UNK     0      -3.498  -3.108   2.995  0.00  0.00           C+0
HETATM   55  O   UNK     0      -2.618  -3.727   3.637  0.00  0.00           O+0
HETATM   56  C   UNK     0      -0.120   0.120   1.824  0.00  0.00           C+0
HETATM   57  O   UNK     0      -0.011   0.641   3.136  0.00  0.00           O+0
HETATM   58  O   UNK     0       2.585   1.118  -1.585  0.00  0.00           O+0
HETATM   59  C   UNK     0       2.671   0.104  -2.521  0.00  0.00           C+0
HETATM   60  C   UNK     0       1.391  -0.681  -2.692  0.00  0.00           C+0
HETATM   61  H   UNK     0       4.353  -3.995  -2.888  0.00  0.00           H+0
HETATM   62  H   UNK     0       5.572  -2.683  -2.540  0.00  0.00           H+0
HETATM   63  H   UNK     0       4.695  -3.523  -1.218  0.00  0.00           H+0
HETATM   64  H   UNK     0       2.787  -2.387  -1.676  0.00  0.00           H+0
HETATM   65  H   UNK     0       4.628  -0.636  -3.138  0.00  0.00           H+0
HETATM   66  H   UNK     0       4.844   0.561  -0.950  0.00  0.00           H+0
HETATM   67  H   UNK     0       6.617   0.280  -0.385  0.00  0.00           H+0
HETATM   68  H   UNK     0       7.120  -3.159  -0.428  0.00  0.00           H+0
HETATM   69  H   UNK     0       8.432  -3.125  -1.656  0.00  0.00           H+0
HETATM   70  H   UNK     0       9.027  -3.347   0.965  0.00  0.00           H+0
HETATM   71  H   UNK     0      10.575  -1.368  -0.290  0.00  0.00           H+0
HETATM   72  H   UNK     0       8.976  -0.381   0.326  0.00  0.00           H+0
HETATM   73  H   UNK     0       9.883  -0.273   2.261  0.00  0.00           H+0
HETATM   74  H   UNK     0       6.731  -2.050   1.548  0.00  0.00           H+0
HETATM   75  H   UNK     0       6.521   0.709   1.656  0.00  0.00           H+0
HETATM   76  H   UNK     0       2.769  -1.466   0.092  0.00  0.00           H+0
HETATM   77  H   UNK     0       3.326   0.066   1.945  0.00  0.00           H+0
HETATM   78  H   UNK     0       2.721   1.469   0.401  0.00  0.00           H+0
HETATM   79  H   UNK     0       1.104   1.746   1.273  0.00  0.00           H+0
HETATM   80  H   UNK     0       0.856   3.248  -0.383  0.00  0.00           H+0
HETATM   81  H   UNK     0       0.639   4.974  -1.568  0.00  0.00           H+0
HETATM   82  H   UNK     0      -0.764   5.958  -1.216  0.00  0.00           H+0
HETATM   83  H   UNK     0      -0.580   4.966  -2.812  0.00  0.00           H+0
HETATM   84  H   UNK     0      -2.331   6.169  -2.665  0.00  0.00           H+0
HETATM   85  H   UNK     0      -5.231   5.612  -2.978  0.00  0.00           H+0
HETATM   86  H   UNK     0      -4.912   5.884  -5.211  0.00  0.00           H+0
HETATM   87  H   UNK     0      -3.113   5.832  -4.835  0.00  0.00           H+0
HETATM   88  H   UNK     0      -4.058   7.407  -4.931  0.00  0.00           H+0
HETATM   89  H   UNK     0      -5.491   9.402  -2.992  0.00  0.00           H+0
HETATM   90  H   UNK     0      -5.005   2.620  -0.910  0.00  0.00           H+0
HETATM   91  H   UNK     0      -1.150  -2.003   2.894  0.00  0.00           H+0
HETATM   92  H   UNK     0      -5.742   0.431   0.050  0.00  0.00           H+0
HETATM   93  H   UNK     0      -7.870  -2.880   1.673  0.00  0.00           H+0
HETATM   94  H   UNK     0     -10.151  -6.447   3.449  0.00  0.00           H+0
HETATM   95  H   UNK     0      -8.515  -7.095   3.131  0.00  0.00           H+0
HETATM   96  H   UNK     0      -8.791  -6.169   4.619  0.00  0.00           H+0
HETATM   97  H   UNK     0      -6.740  -6.159   4.126  0.00  0.00           H+0
HETATM   98  H   UNK     0      -4.410  -6.335   4.867  0.00  0.00           H+0
HETATM   99  H   UNK     0       0.482  -0.821   1.851  0.00  0.00           H+0
HETATM  100  H   UNK     0      -0.265  -0.037   3.802  0.00  0.00           H+0
HETATM  101  H   UNK     0       2.825   0.626  -3.509  0.00  0.00           H+0
HETATM  102  H   UNK     0       1.094  -1.276  -1.832  0.00  0.00           H+0
HETATM  103  H   UNK     0       1.466  -1.285  -3.633  0.00  0.00           H+0
HETATM  104  H   UNK     0       0.584   0.055  -2.898  0.00  0.00           H+0
CONECT    1    2   61   62   63                                             
CONECT    2    1    3   64                                                  
CONECT    3    2    4   59   65                                             
CONECT    4    3    5   15   66                                             
CONECT    5    4    6                                                       
CONECT    6    5    7   13   67                                             
CONECT    7    6    8                                                       
CONECT    8    7    9   68   69                                             
CONECT    9    8   10   11   70                                             
CONECT   10    9   71                                                       
CONECT   11    9   12   13   72                                             
CONECT   12   11   73                                                       
CONECT   13   11   14    6   74                                             
CONECT   14   13   75                                                       
CONECT   15    4   16   17   76                                             
CONECT   16   15   77                                                       
CONECT   17   15   18   58   78                                             
CONECT   18   17   19                                                       
CONECT   19   18   20   56   79                                             
CONECT   20   19   21   35                                                  
CONECT   21   20   22   80                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22   81   82   83                                             
CONECT   24   22   25   33                                                  
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   28   84                                                  
CONECT   28   27   29   30   85                                             
CONECT   29   28   86   87   88                                             
CONECT   30   28   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   89                                                       
CONECT   33   24   34   35                                                  
CONECT   34   33   90                                                       
CONECT   35   33   36   20                                                  
CONECT   36   35   37   41                                                  
CONECT   37   36   38   56                                                  
CONECT   38   37   39   91                                                  
CONECT   39   38   40   54                                                  
CONECT   40   39   41   43                                                  
CONECT   41   40   42   36                                                  
CONECT   42   41   92                                                       
CONECT   43   40   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   46   53                                                  
CONECT   46   45   47   93                                                  
CONECT   47   46   48   50                                                  
CONECT   48   47   49                                                       
CONECT   49   48   94   95   96                                             
CONECT   50   47   51   97                                                  
CONECT   51   50   52   53                                                  
CONECT   52   51   98                                                       
CONECT   53   51   54   45                                                  
CONECT   54   53   55   39                                                  
CONECT   55   54                                                            
CONECT   56   37   57   19   99                                             
CONECT   57   56  100                                                       
CONECT   58   17   59                                                       
CONECT   59   58   60    3  101                                             
CONECT   60   59  102  103  104                                             
CONECT   61    1                                                            
CONECT   62    1                                                            
CONECT   63    1                                                            
CONECT   64    2                                                            
CONECT   65    3                                                            
CONECT   66    4                                                            
CONECT   67    6                                                            
CONECT   68    8                                                            
CONECT   69    8                                                            
CONECT   70    9                                                            
CONECT   71   10                                                            
CONECT   72   11                                                            
CONECT   73   12                                                            
CONECT   74   13                                                            
CONECT   75   14                                                            
CONECT   76   15                                                            
CONECT   77   16                                                            
CONECT   78   17                                                            
CONECT   79   19                                                            
CONECT   80   21                                                            
CONECT   81   23                                                            
CONECT   82   23                                                            
CONECT   83   23                                                            
CONECT   84   27                                                            
CONECT   85   28                                                            
CONECT   86   29                                                            
CONECT   87   29                                                            
CONECT   88   29                                                            
CONECT   89   32                                                            
CONECT   90   34                                                            
CONECT   91   38                                                            
CONECT   92   42                                                            
CONECT   93   46                                                            
CONECT   94   49                                                            
CONECT   95   49                                                            
CONECT   96   49                                                            
CONECT   97   50                                                            
CONECT   98   52                                                            
CONECT   99   56                                                            
CONECT  100   57                                                            
CONECT  101   59                                                            
CONECT  102   60                                                            
CONECT  103   60                                                            
CONECT  104   60                                                            
MASTER        0    0    0    0    0    0    0    0  104    0  220    0
END

RDKit          3D

104110  0  0  0  0  0  0  0  0999 V2000
    4.5964   -3.1042   -2.2335 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5136   -2.1916   -2.3842 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8746   -0.7948   -2.3250 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.4433   -0.4998   -0.9686 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.4045   -1.4021   -0.5625 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6239   -0.8216   -0.2506 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5296   -1.3364   -1.1837 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9763   -2.6047   -0.8170 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0330   -2.4923    0.2887 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.2520   -2.2823   -0.3504 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6735   -1.2000    1.0150 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.2827   -1.0788    2.2392 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.1428   -1.1103    1.1135 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.9112   -0.1034    2.0484 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3135   -0.5226    0.0256 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.9305   -0.3287    1.2890 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3931    0.6463   -0.2878 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.0697    0.3285   -0.1565 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3701    1.0529    0.8111 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.6816    1.9001    0.1951 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2291    3.0349   -0.4308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1216    3.8501   -1.0793 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4960    5.0438   -1.7313 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4671    3.5854   -1.1339 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3856    4.4242   -1.8325 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6277    4.0564   -1.8610 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1673    5.6170   -2.5137 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3726    6.2599   -3.1606 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.0670    6.3294   -4.6197 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5510    7.6024   -2.5558 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7855    8.0394   -1.6712 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5956    8.3835   -2.9889 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9375    2.4092   -0.4824 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2364    2.1625   -0.5297 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0491    1.5889    0.1668 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4933    0.4190    0.9395 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5333   -0.2693    1.6497 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8870   -1.4201    2.3135 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1792   -1.8822    2.2741 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1253   -1.1801    1.5591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7946   -0.0048    0.8716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7974    0.5822    0.2105 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4751   -1.7223    1.5546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3984   -1.1401    0.9246 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7953   -2.9604    2.2823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0882   -3.4149    2.2331 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4325   -4.5663    2.8957 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7602   -5.0420    2.8513 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0693   -6.2318    3.5471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4655   -5.2453    3.6009 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1642   -4.8206    3.6721 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1669   -5.4827    4.3744 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8462   -3.6416    2.9841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4984   -3.1084    2.9947 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6177   -3.7270    3.6369 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1195    0.1197    1.8242 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0110    0.6412    3.1357 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.4103   -6.3347    4.8669 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

View in JSmol View NMR Assignments

Synonyms

Not Available

Chemical Formula

C₄₀H₄₄N₂O₁₈

Average Mass

840.7880 Da

Monoisotopic Mass

840.25891 Da

IUPAC Name

(2R)-2-{[(10S,11S)-2,5,11,17-tetrahydroxy-10-{[(2S,3R,4S,5S,6R)-3-hydroxy-6-methyl-5-(methylamino)-4-{[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy}oxan-2-yl]oxy}-19-methoxy-7-methyl-15,22-dioxopentacyclo[12.8.0.0^{3,12}.0^{4,9}.0^{16,21}]docosa-1,3(12),4,6,8,13,16,18,20-nonaen-6-yl]formamido}propanoic acid

Traditional Name

CAS Registry Number

Not Available

SMILES

CN[C@H]1[C@@H](C)O[C@@H](O[C@@H]2[C@@H](O)C3=C(C(O)=C4C(=O)C5=CC(OC)=CC(O)=C5C(=O)C4=C3)C3=C(O)C(C(=O)N[C@H](C)C(O)=O)=C(C)C=C23)[C@H](O)[C@H]1O[C@@H]1OC[C@@H](O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C40H44N2O18/c1-11-6-18-24(31(49)21(11)37(53)42-12(2)38(54)55)23-16(9-17-25(32(23)50)28(46)15-7-14(56-5)8-19(43)22(15)27(17)45)29(47)35(18)59-40-34(52)36(26(41-4)13(3)58-40)60-39-33(51)30(48)20(44)10-57-39/h6-9,12-13,20,26,29-30,33-36,39-41,43-44,47-52H,10H2,1-5H3,(H,42,53)(H,54,55)/t12-,13-,20-,26+,29+,30+,33-,34-,35+,36+,39+,40+/m1/s1

InChI Key

WPICPWIIIBCXCV-NJGWPHBESA-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
Actinomadura hibisca	NPAtlas	2387769

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	0.79	ALOGPS
logP	-0.52	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	2.74	ChemAxon
pKa (Strongest Basic)	9	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	19	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	320.56 Å²	ChemAxon
Rotatable Bond Count	9	ChemAxon
Refractivity	203.04 m³·mol⁻¹	ChemAxon
Polarizability	86.4 Å³	ChemAxon
Number of Rings	7	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

NPA008193

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

4586139

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5479145

PDB ID

Not Available

ChEBI ID

8349

Good Scents ID

Not Available

References

General References

Tomita K, Nishio M, Saitoh K, Yamamoto H, Hoshino Y, Ohkuma H, Konishi M, Miyaki T, Oki T: Pradimicins A, B and C: new antifungal antibiotics. I. Taxonomy, production, isolation and physico-chemical properties. J Antibiot (Tokyo). 1990 Jul;43(7):755-62. doi: 10.7164/antibiotics.43.755. [PubMed:2387769 ]
Oki T, Tenmyo O, Hirano M, Tomatsu K, Kamei H: Pradimicins A, B and C: new antifungal antibiotics. II. In vitro and in vivo biological activities. J Antibiot (Tokyo). 1990 Jul;43(7):763-70. doi: 10.7164/antibiotics.43.763. [PubMed:2167304 ]
Balzarini J, Van Laethem K, Daelemans D, Hatse S, Bugatti A, Rusnati M, Igarashi Y, Oki T, Schols D: Pradimicin A, a carbohydrate-binding nonpeptidic lead compound for treatment of infections with viruses with highly glycosylated envelopes, such as human immunodeficiency virus. J Virol. 2007 Jan;81(1):362-73. doi: 10.1128/JVI.01404-06. Epub 2006 Oct 18. [PubMed:17050611 ]
Nakagawa Y, Masuda Y, Yamada K, Doi T, Takegoshi K, Igarashi Y, Ito Y: Solid-state NMR spectroscopic analysis of the Ca2+-dependent mannose binding of pradimicin A. Angew Chem Int Ed Engl. 2011 Jun 27;50(27):6084-8. doi: 10.1002/anie.201007775. Epub 2011 May 19. [PubMed:21598364 ]
Nakagawa Y, Doi T, Masuda Y, Takegoshi K, Igarashi Y, Ito Y: Mapping of the primary mannose binding site of pradimicin A. J Am Chem Soc. 2011 Nov 2;133(43):17485-93. doi: 10.1021/ja207816h. Epub 2011 Oct 6. [PubMed:21942374 ]

Showing NP-Card for Pradimicin A (NP0011950)

MOL for NP0011950 (Pradimicin A)

3D MOL for NP0011950 (Pradimicin A)

3D SDF for NP0011950 (Pradimicin A)

3D-SDF for NP0011950 (Pradimicin A)

PDB for NP0011950 (Pradimicin A)

3D PDB for NP0011950 (Pradimicin A)

SMILES for NP0011950 (Pradimicin A)

INCHI for NP0011950 (Pradimicin A)

Structure for NP0011950 (Pradimicin A)

3D Structure for NP0011950 (Pradimicin A)