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Showing NP-Card for Micrococcin P1 (NP0023971)

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Record Information
Version2.0
Created at2021-05-03 15:42:31 UTC
Updated at2021-07-26 15:24:08 UTC
NP-MRD IDNP0023971
Secondary Accession NumbersNone
Natural Product Identification
Common NameMicrococcin P1
Provided ByJEOL DatabaseJEOL Logo
DescriptionMicrococcin P1 is a macrocyclic thiopeptide antibiotic of the thiocillin-thiazolyl class that contains 6 thiazole rings. It has been found to be produced by the food-borne bacterium Staphylococcus equorum WS 2733. Tests indicate that Micrococcin P1 inhibits Listeria monocytogenes and a number of other gram-positive bacteria. In fact, in a detailed bactericidal study conducted in 2000, a total of 95 out of 95 Listeria strains and 130 out of 138 other gram-positive bacteria were inhibited by this peptide (PMID: 10831414 ). Nearly all gram-positive bacteria tested were sensitive, whereas no inhibition of 37 gram-negative bacteria was observed (PMID: 10831414 ). The antibacterial activity of the peptide arises from its binding to complexes formed between the L11 protein of the 50S ribosomal subunit and a nucleotide sequence within the 23S rRNA. This inhibits the elongation factor EFG-dependent translocation step of the growing peptide chain (PMID: 10831414 ). Resistant mutants of B. Subtilis and B.Megaterium either possess a structurally altered 50S subunit or are specifically methylated at a single site (nucleotide A-1067) of the 23S rRNA. It has been shown that micrococcin P1 is synthesized non ribosomally and involves a multifunctional peptide synthetase called micrococcin synthase (PMID: 10831414 ). Micrococcin P1 has been purified from a bacterium related to Micrococcus varians and from Bacillus pumilus, isolated from sewage and soil, respectively (PMID: 10831414 ).
Structure
Data?1623995044
MOL3D MOLSDF3D SDFPDBSMILESInChI

MOL for NP0023971 (Micrococcin P1)


  Mrv1652306102103383D          

125132  0  0  0  0            999 V2000
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    1.5685   -1.0851    1.3039 N   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for NP0023971 (Micrococcin P1)

     RDKit          3D

125132  0  0  0  0  0  0  0  0999 V2000
    3.2850   -6.3924   -4.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2384   -7.4949   -4.5276 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1911   -8.0449   -3.7517 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4316   -7.6224   -2.4645 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2721   -8.1720   -1.5185 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0194   -9.1300   -1.6738 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for NP0023971 (Micrococcin P1)


  Mrv1652306102103383D          

125132  0  0  0  0            999 V2000
    3.2850   -6.3924   -4.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.6882    6.6905   -1.6075 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9166    6.3282   -1.1233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9082    6.8054   -1.6782 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0481    5.4326    0.0293 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2430    4.8158    0.3534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1176    4.0012    1.8485 S   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4771    4.5487    2.0090 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0330    5.2047    0.9533 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7493    4.3166    3.2246 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2160    4.9146    4.3429 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6604    4.8679    5.7330 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5559    3.6332    3.2566 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8544    2.8614    2.3823 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7268    2.5052    2.7601 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3985    2.3745    1.0316 C   0  0  2  0  0  0  0  0  0  0  0  0
   -6.4713    1.2864    1.2419 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.2715    0.9979   -0.0233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8780    0.0542    1.6733 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2454    1.8430    0.2997 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0716    1.9597   -1.0520 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9050    2.4416   -1.8111 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7670    1.4631   -1.4892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2258    1.6788   -2.7406 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6560    1.0059   -2.8274 S   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8221    0.4074   -1.2180 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9578    0.7184   -0.6281 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6926   -3.9896    0.6689 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.3351   -6.3502   -0.1059 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.9747   -9.1518   -4.4087 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4214  -10.0984   -4.9580 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.3328   -8.9603   -4.3966 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.2501   -9.9364   -4.9557 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.4545  -11.1352   -4.0173 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.4303  -12.1384   -4.6124 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.9923  -10.6810   -2.7713 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2568   -6.7493   -4.3118 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4346   -5.5567   -4.8858 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3897   -6.0087   -3.1780 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1098   -7.8928   -5.5361 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8850   -6.8426   -2.1076 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1786   -4.3446    3.6808 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1636   -3.1514   -1.2999 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4864   -1.6938   -2.3569 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
NP0023971

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]O[C@]([H])(C([H])([H])[H])C([H])([H])N([H])C(=O)C(\N([H])C(=O)C1=C([H])SC(=N1)C1=C([H])SC(=N1)C1=C([H])C([H])=C2C3=NC(=C([H])S3)C(=O)N([H])[C@]([H])(C(=O)N([H])\C(=C(\[H])C([H])([H])[H])C3=NC(=C([H])S3)C(=O)N([H])[C@]([H])(C3=NC(=C([H])S3)C(=O)N([H])[C@@]([H])(C3=NC(=C([H])S3)C2=N1)[C@]([H])(O[H])C([H])([H])[H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@]([H])(O[H])C([H])([H])[H])=C(/[H])C([H])([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C48H49N13O9S6/c1-8-24(37(65)49-12-20(5)62)51-38(66)28-15-73-46(56-28)32-18-74-45(58-32)26-11-10-23-36(50-26)27-13-75-48(53-27)35(22(7)64)61-41(69)31-17-76-47(57-31)33(19(3)4)59-39(67)30-16-72-44(55-30)25(9-2)52-42(70)34(21(6)63)60-40(68)29-14-71-43(23)54-29/h8-11,13-22,33-35,62-64H,12H2,1-7H3,(H,49,65)(H,51,66)(H,52,70)(H,59,67)(H,60,68)(H,61,69)/b24-8-,25-9-/t20-,21-,22-,33+,34+,35-/m1/s1

> <INCHI_KEY>
MQGFYNRGFWXAKA-SRPYWAJFSA-N

> <FORMULA>
C48H49N13O9S6

> <MOLECULAR_WEIGHT>
1144.36

> <EXACT_MASS>
1143.210047254

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
125

> <JCHEM_AVERAGE_POLARIZABILITY>
118.26160866408921

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2Z)-2-[(2-{2-[(12R,19S,26Z,29S)-26-ethylidene-12,29-bis[(1R)-1-hydroxyethyl]-14,21,28,31-tetraoxo-19-(propan-2-yl)-10,17,24,34-tetrathia-6,13,20,27,30,35,36,37,38-nonaazahexacyclo[30.2.1.1^{8,11}.1^{15,18}.1^{22,25}.0^{2,7}]octatriaconta-1(35),2,4,6,8,11(38),15,18(37),22,25(36),32-undecaen-5-yl]-1,3-thiazol-4-yl}-1,3-thiazol-4-yl)formamido]-N-[(2R)-2-hydroxypropyl]but-2-enamide

> <ALOGPS_LOGP>
4.23

> <JCHEM_LOGP>
3.905070219999997

> <ALOGPS_LOGS>
-5.24

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.72580266525738

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.928297497503626

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5263516818961893

> <JCHEM_POLAR_SURFACE_AREA>
325.5199999999999

> <JCHEM_REFRACTIVITY>
316.1709000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
6.56e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
Micrococcin P1

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0023971 (Micrococcin P1)

     RDKit          3D

125132  0  0  0  0  0  0  0  0999 V2000
    3.2850   -6.3924   -4.1950 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2384   -7.4949   -4.5276 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1911   -8.0449   -3.7517 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4316   -7.6224   -2.4645 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.2721   -8.1720   -1.5185 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0194   -9.1300   -1.6738 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1840   -7.4507   -0.2437 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8994   -7.7721    0.8937 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5084   -6.6875    2.1599 S   0  0  0  0  0  0  0  0  0  0  0  0
    5.4174   -5.8649    1.1171 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5574   -4.6101    1.5594 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5963   -4.0523    2.8192 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5267   -2.7173    2.8982 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.0825   -2.9706    1.2491 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0969   -2.0999    0.5808 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7331   -2.3261   -0.7391 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7908   -1.4868   -1.3327 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -0.4184   -0.6138 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6566   -0.2588    0.7073 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5685   -1.0851    1.3039 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.2173    0.8347    1.5738 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1041    0.6290    2.9019 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for NP0023971 (Micrococcin P1)

HEADER    PROTEIN                                 10-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-JUN-21         0                                  
HETATM    1  C   UNK     0       3.285  -6.392  -4.195  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.238  -7.495  -4.528  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.191  -8.045  -3.752  0.00  0.00           C+0
HETATM    4  N   UNK     0       5.432  -7.622  -2.465  0.00  0.00           N+0
HETATM    5  C   UNK     0       6.272  -8.172  -1.519  0.00  0.00           C+0
HETATM    6  O   UNK     0       7.019  -9.130  -1.674  0.00  0.00           O+0
HETATM    7  C   UNK     0       6.184  -7.451  -0.244  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.899  -7.772   0.894  0.00  0.00           C+0
HETATM    9  S   UNK     0       6.508  -6.688   2.160  0.00  0.00           S+0
HETATM   10  C   UNK     0       5.417  -5.865   1.117  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.557  -4.610   1.559  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.596  -4.052   2.819  0.00  0.00           C+0
HETATM   13  S   UNK     0       3.527  -2.717   2.898  0.00  0.00           S+0
HETATM   14  C   UNK     0       3.083  -2.971   1.249  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.097  -2.100   0.581  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.733  -2.326  -0.739  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.791  -1.487  -1.333  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.228  -0.418  -0.614  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.657  -0.259   0.707  0.00  0.00           C+0
HETATM   20  N   UNK     0       1.569  -1.085   1.304  0.00  0.00           N+0
HETATM   21  C   UNK     0       0.217   0.835   1.574  0.00  0.00           C+0
HETATM   22  C   UNK     0      -0.104   0.629   2.902  0.00  0.00           C+0
HETATM   23  S   UNK     0      -0.437   2.120   3.668  0.00  0.00           S+0
HETATM   24  C   UNK     0      -0.128   2.940   2.184  0.00  0.00           C+0
HETATM   25  N   UNK     0       0.181   2.162   1.159  0.00  0.00           N+0
HETATM   26  C   UNK     0      -0.144   4.452   2.151  0.00  0.00           C+0
HETATM   27  C   UNK     0       0.932   5.023   1.181  0.00  0.00           C+0
HETATM   28  C   UNK     0       2.360   4.684   1.595  0.00  0.00           C+0
HETATM   29  O   UNK     0       0.726   4.580  -0.171  0.00  0.00           O+0
HETATM   30  N   UNK     0      -1.463   4.916   1.754  0.00  0.00           N+0
HETATM   31  C   UNK     0      -1.997   6.075   2.261  0.00  0.00           C+0
HETATM   32  O   UNK     0      -1.504   6.689   3.203  0.00  0.00           O+0
HETATM   33  C   UNK     0      -3.177   6.548   1.535  0.00  0.00           C+0
HETATM   34  C   UNK     0      -3.840   7.725   1.829  0.00  0.00           C+0
HETATM   35  S   UNK     0      -5.071   8.019   0.680  0.00  0.00           S+0
HETATM   36  C   UNK     0      -4.673   6.545  -0.122  0.00  0.00           C+0
HETATM   37  N   UNK     0      -3.689   5.859   0.436  0.00  0.00           N+0
HETATM   38  C   UNK     0      -5.366   6.092  -1.396  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.482   6.342  -2.660  0.00  0.00           C+0
HETATM   40  C   UNK     0      -3.201   5.503  -2.670  0.00  0.00           C+0
HETATM   41  C   UNK     0      -4.115   7.815  -2.888  0.00  0.00           C+0
HETATM   42  N   UNK     0      -6.688   6.691  -1.607  0.00  0.00           N+0
HETATM   43  C   UNK     0      -7.917   6.328  -1.123  0.00  0.00           C+0
HETATM   44  O   UNK     0      -8.908   6.805  -1.678  0.00  0.00           O+0
HETATM   45  C   UNK     0      -8.048   5.433   0.029  0.00  0.00           C+0
HETATM   46  C   UNK     0      -9.243   4.816   0.353  0.00  0.00           C+0
HETATM   47  S   UNK     0      -9.118   4.001   1.849  0.00  0.00           S+0
HETATM   48  C   UNK     0      -7.477   4.549   2.009  0.00  0.00           C+0
HETATM   49  N   UNK     0      -7.033   5.205   0.953  0.00  0.00           N+0
HETATM   50  C   UNK     0      -6.749   4.317   3.225  0.00  0.00           C+0
HETATM   51  C   UNK     0      -7.216   4.915   4.343  0.00  0.00           C+0
HETATM   52  C   UNK     0      -6.660   4.868   5.733  0.00  0.00           C+0
HETATM   53  N   UNK     0      -5.556   3.633   3.257  0.00  0.00           N+0
HETATM   54  C   UNK     0      -4.854   2.861   2.382  0.00  0.00           C+0
HETATM   55  O   UNK     0      -3.727   2.505   2.760  0.00  0.00           O+0
HETATM   56  C   UNK     0      -5.399   2.374   1.032  0.00  0.00           C+0
HETATM   57  C   UNK     0      -6.471   1.286   1.242  0.00  0.00           C+0
HETATM   58  C   UNK     0      -7.271   0.998  -0.023  0.00  0.00           C+0
HETATM   59  O   UNK     0      -5.878   0.054   1.673  0.00  0.00           O+0
HETATM   60  N   UNK     0      -4.245   1.843   0.300  0.00  0.00           N+0
HETATM   61  C   UNK     0      -4.072   1.960  -1.052  0.00  0.00           C+0
HETATM   62  O   UNK     0      -4.905   2.442  -1.811  0.00  0.00           O+0
HETATM   63  C   UNK     0      -2.767   1.463  -1.489  0.00  0.00           C+0
HETATM   64  C   UNK     0      -2.226   1.679  -2.741  0.00  0.00           C+0
HETATM   65  S   UNK     0      -0.656   1.006  -2.827  0.00  0.00           S+0
HETATM   66  C   UNK     0      -0.822   0.407  -1.218  0.00  0.00           C+0
HETATM   67  N   UNK     0      -1.958   0.718  -0.628  0.00  0.00           N+0
HETATM   68  N   UNK     0       3.693  -3.990   0.669  0.00  0.00           N+0
HETATM   69  N   UNK     0       5.335  -6.350  -0.106  0.00  0.00           N+0
HETATM   70  C   UNK     0       5.975  -9.152  -4.409  0.00  0.00           C+0
HETATM   71  O   UNK     0       5.421 -10.098  -4.958  0.00  0.00           O+0
HETATM   72  N   UNK     0       7.333  -8.960  -4.397  0.00  0.00           N+0
HETATM   73  C   UNK     0       8.250  -9.936  -4.956  0.00  0.00           C+0
HETATM   74  C   UNK     0       8.454 -11.135  -4.017  0.00  0.00           C+0
HETATM   75  C   UNK     0       9.430 -12.138  -4.612  0.00  0.00           C+0
HETATM   76  O   UNK     0       8.992 -10.681  -2.771  0.00  0.00           O+0
HETATM   77  H   UNK     0       2.257  -6.749  -4.312  0.00  0.00           H+0
HETATM   78  H   UNK     0       3.435  -5.557  -4.886  0.00  0.00           H+0
HETATM   79  H   UNK     0       3.390  -6.009  -3.178  0.00  0.00           H+0
HETATM   80  H   UNK     0       4.110  -7.893  -5.536  0.00  0.00           H+0
HETATM   81  H   UNK     0       4.885  -6.843  -2.108  0.00  0.00           H+0
HETATM   82  H   UNK     0       7.612  -8.575   1.030  0.00  0.00           H+0
HETATM   83  H   UNK     0       5.179  -4.345   3.681  0.00  0.00           H+0
HETATM   84  H   UNK     0       2.164  -3.151  -1.300  0.00  0.00           H+0
HETATM   85  H   UNK     0       0.486  -1.694  -2.357  0.00  0.00           H+0
HETATM   86  H   UNK     0      -0.131  -0.303   3.450  0.00  0.00           H+0
HETATM   87  H   UNK     0       0.078   4.840   3.154  0.00  0.00           H+0
HETATM   88  H   UNK     0       0.837   6.115   1.158  0.00  0.00           H+0
HETATM   89  H   UNK     0       2.566   5.013   2.618  0.00  0.00           H+0
HETATM   90  H   UNK     0       3.072   5.174   0.922  0.00  0.00           H+0
HETATM   91  H   UNK     0       2.560   3.610   1.522  0.00  0.00           H+0
HETATM   92  H   UNK     0       0.646   3.603  -0.132  0.00  0.00           H+0
HETATM   93  H   UNK     0      -1.925   4.495   0.954  0.00  0.00           H+0
HETATM   94  H   UNK     0      -3.631   8.424   2.627  0.00  0.00           H+0
HETATM   95  H   UNK     0      -5.535   5.012  -1.308  0.00  0.00           H+0
HETATM   96  H   UNK     0      -5.073   6.022  -3.530  0.00  0.00           H+0
HETATM   97  H   UNK     0      -3.426   4.450  -2.495  0.00  0.00           H+0
HETATM   98  H   UNK     0      -2.704   5.576  -3.643  0.00  0.00           H+0
HETATM   99  H   UNK     0      -2.485   5.833  -1.912  0.00  0.00           H+0
HETATM  100  H   UNK     0      -3.601   7.932  -3.849  0.00  0.00           H+0
HETATM  101  H   UNK     0      -3.441   8.190  -2.111  0.00  0.00           H+0
HETATM  102  H   UNK     0      -4.999   8.457  -2.914  0.00  0.00           H+0
HETATM  103  H   UNK     0      -6.771   7.394  -2.328  0.00  0.00           H+0
HETATM  104  H   UNK     0     -10.174   4.844  -0.198  0.00  0.00           H+0
HETATM  105  H   UNK     0      -8.119   5.523   4.275  0.00  0.00           H+0
HETATM  106  H   UNK     0      -6.248   5.845   6.001  0.00  0.00           H+0
HETATM  107  H   UNK     0      -7.466   4.635   6.437  0.00  0.00           H+0
HETATM  108  H   UNK     0      -5.884   4.112   5.874  0.00  0.00           H+0
HETATM  109  H   UNK     0      -5.016   3.722   4.109  0.00  0.00           H+0
HETATM  110  H   UNK     0      -5.786   3.218   0.465  0.00  0.00           H+0
HETATM  111  H   UNK     0      -7.168   1.581   2.031  0.00  0.00           H+0
HETATM  112  H   UNK     0      -7.718   1.908  -0.435  0.00  0.00           H+0
HETATM  113  H   UNK     0      -8.075   0.287   0.196  0.00  0.00           H+0
HETATM  114  H   UNK     0      -6.651   0.527  -0.793  0.00  0.00           H+0
HETATM  115  H   UNK     0      -5.145  -0.132   1.057  0.00  0.00           H+0
HETATM  116  H   UNK     0      -3.449   1.513   0.848  0.00  0.00           H+0
HETATM  117  H   UNK     0      -2.661   2.215  -3.573  0.00  0.00           H+0
HETATM  118  H   UNK     0       7.716  -8.178  -3.884  0.00  0.00           H+0
HETATM  119  H   UNK     0       7.864 -10.268  -5.926  0.00  0.00           H+0
HETATM  120  H   UNK     0       9.197  -9.408  -5.115  0.00  0.00           H+0
HETATM  121  H   UNK     0       7.502 -11.635  -3.807  0.00  0.00           H+0
HETATM  122  H   UNK     0      10.412 -11.681  -4.777  0.00  0.00           H+0
HETATM  123  H   UNK     0       9.063 -12.535  -5.564  0.00  0.00           H+0
HETATM  124  H   UNK     0       9.586 -12.975  -3.922  0.00  0.00           H+0
HETATM  125  H   UNK     0       8.273 -10.155  -2.354  0.00  0.00           H+0
CONECT    1    2   77   78   79                                             
CONECT    2    3    1   80                                                  
CONECT    3    4   70    2                                                  
CONECT    4    5    3   81                                                  
CONECT    5    7    6    4                                                  
CONECT    6    5                                                            
CONECT    7   69    8    5                                                  
CONECT    8    7    9   82                                                  
CONECT    9    8   10                                                       
CONECT   10   11   69    9                                                  
CONECT   11   12   68   10                                                  
CONECT   12   13   11   83                                                  
CONECT   13   14   12                                                       
CONECT   14   15   13   68                                                  
CONECT   15   16   14   20                                                  
CONECT   16   15   17   84                                                  
CONECT   17   16   18   85                                                  
CONECT   18   17   19   66                                                  
CONECT   19   20   18   21                                                  
CONECT   20   19   15                                                       
CONECT   21   25   22   19                                                  
CONECT   22   23   21   86                                                  
CONECT   23   24   22                                                       
CONECT   24   25   23   26                                                  
CONECT   25   21   24                                                       
CONECT   26   30   27   24   87                                             
CONECT   27   26   29   28   88                                             
CONECT   28   27   89   90   91                                             
CONECT   29   27   92                                                       
CONECT   30   31   26   93                                                  
CONECT   31   33   32   30                                                  
CONECT   32   31                                                            
CONECT   33   37   34   31                                                  
CONECT   34   33   35   94                                                  
CONECT   35   34   36                                                       
CONECT   36   38   37   35                                                  
CONECT   37   36   33                                                       
CONECT   38   42   39   36   95                                             
CONECT   39   38   40   41   96                                             
CONECT   40   39   97   98   99                                             
CONECT   41   39  100  101  102                                             
CONECT   42   43   38  103                                                  
CONECT   43   42   44   45                                                  
CONECT   44   43                                                            
CONECT   45   46   49   43                                                  
CONECT   46   47   45  104                                                  
CONECT   47   48   46                                                       
CONECT   48   50   47   49                                                  
CONECT   49   45   48                                                       
CONECT   50   53   51   48                                                  
CONECT   51   50   52  105                                                  
CONECT   52   51  106  107  108                                             
CONECT   53   54   50  109                                                  
CONECT   54   56   53   55                                                  
CONECT   55   54                                                            
CONECT   56   54   57   60  110                                             
CONECT   57   56   58   59  111                                             
CONECT   58   57  112  113  114                                             
CONECT   59   57  115                                                       
CONECT   60   61   56  116                                                  
CONECT   61   63   62   60                                                  
CONECT   62   61                                                            
CONECT   63   61   64   67                                                  
CONECT   64   65   63  117                                                  
CONECT   65   66   64                                                       
CONECT   66   65   67   18                                                  
CONECT   67   63   66                                                       
CONECT   68   11   14                                                       
CONECT   69   10    7                                                       
CONECT   70    3   71   72                                                  
CONECT   71   70                                                            
CONECT   72   70   73  118                                                  
CONECT   73   72   74  119  120                                             
CONECT   74   73   75   76  121                                             
CONECT   75   74  122  123  124                                             
CONECT   76   74  125                                                       
CONECT   77    1                                                            
CONECT   78    1                                                            
CONECT   79    1                                                            
CONECT   80    2                                                            
CONECT   81    4                                                            
CONECT   82    8                                                            
CONECT   83   12                                                            
CONECT   84   16                                                            
CONECT   85   17                                                            
CONECT   86   22                                                            
CONECT   87   26                                                            
CONECT   88   27                                                            
CONECT   89   28                                                            
CONECT   90   28                                                            
CONECT   91   28                                                            
CONECT   92   29                                                            
CONECT   93   30                                                            
CONECT   94   34                                                            
CONECT   95   38                                                            
CONECT   96   39                                                            
CONECT   97   40                                                            
CONECT   98   40                                                            
CONECT   99   40                                                            
CONECT  100   41                                                            
CONECT  101   41                                                            
CONECT  102   41                                                            
CONECT  103   42                                                            
CONECT  104   46                                                            
CONECT  105   51                                                            
CONECT  106   52                                                            
CONECT  107   52                                                            
CONECT  108   52                                                            
CONECT  109   53                                                            
CONECT  110   56                                                            
CONECT  111   57                                                            
CONECT  112   58                                                            
CONECT  113   58                                                            
CONECT  114   58                                                            
CONECT  115   59                                                            
CONECT  116   60                                                            
CONECT  117   64                                                            
CONECT  118   72                                                            
CONECT  119   73                                                            
CONECT  120   73                                                            
CONECT  121   74                                                            
CONECT  122   75                                                            
CONECT  123   75                                                            
CONECT  124   75                                                            
CONECT  125   76                                                            
MASTER        0    0    0    0    0    0    0    0  125    0  264    0
END
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3D PDB for NP0023971 (Micrococcin P1)

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SMILES for NP0023971 (Micrococcin P1)
[H]O[C@]([H])(C([H])([H])[H])C([H])([H])N([H])C(=O)C(\N([H])C(=O)C1=C([H])SC(=N1)C1=C([H])SC(=N1)C1=C([H])C([H])=C2C3=NC(=C([H])S3)C(=O)N([H])[C@]([H])(C(=O)N([H])\C(=C(\[H])C([H])([H])[H])C3=NC(=C([H])S3)C(=O)N([H])[C@]([H])(C3=NC(=C([H])S3)C(=O)N([H])[C@@]([H])(C3=NC(=C([H])S3)C2=N1)[C@]([H])(O[H])C([H])([H])[H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@]([H])(O[H])C([H])([H])[H])=C(/[H])C([H])([H])[H]
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INCHI for NP0023971 (Micrococcin P1)
InChI=1S/C48H49N13O9S6/c1-8-24(37(65)49-12-20(5)62)51-38(66)28-15-73-46(56-28)32-18-74-45(58-32)26-11-10-23-36(50-26)27-13-75-48(53-27)35(22(7)64)61-41(69)31-17-76-47(57-31)33(19(3)4)59-39(67)30-16-72-44(55-30)25(9-2)52-42(70)34(21(6)63)60-40(68)29-14-71-43(23)54-29/h8-11,13-22,33-35,62-64H,12H2,1-7H3,(H,49,65)(H,51,66)(H,52,70)(H,59,67)(H,60,68)(H,61,69)/b24-8-,25-9-/t20-,21-,22-,33+,34+,35-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC48H49N13O9S6
Average Mass1144.3600 Da
Monoisotopic Mass1143.21005 Da
IUPAC Name(2Z)-2-[(2-{2-[(12R,19S,26Z,29S)-26-ethylidene-12,29-bis[(1R)-1-hydroxyethyl]-14,21,28,31-tetraoxo-19-(propan-2-yl)-10,17,24,34-tetrathia-6,13,20,27,30,35,36,37,38-nonaazahexacyclo[30.2.1.1^{8,11}.1^{15,18}.1^{22,25}.0^{2,7}]octatriaconta-1(35),2,4,6,8,11(38),15,18(37),22,25(36),32-undecaen-5-yl]-1,3-thiazol-4-yl}-1,3-thiazol-4-yl)formamido]-N-[(2R)-2-hydroxypropyl]but-2-enamide
Traditional NameMicrococcin P1
CAS Registry Number67401-56-3
SMILES
[H]O[C@]([H])(C([H])([H])[H])C([H])([H])N([H])C(=O)C(\N([H])C(=O)C1=C([H])SC(=N1)C1=C([H])SC(=N1)C1=C([H])C([H])=C2C3=NC(=C([H])S3)C(=O)N([H])[C@]([H])(C(=O)N([H])\C(=C(\[H])C([H])([H])[H])C3=NC(=C([H])S3)C(=O)N([H])[C@]([H])(C3=NC(=C([H])S3)C(=O)N([H])[C@@]([H])(C3=NC(=C([H])S3)C2=N1)[C@]([H])(O[H])C([H])([H])[H])C([H])(C([H])([H])[H])C([H])([H])[H])[C@]([H])(O[H])C([H])([H])[H])=C(/[H])C([H])([H])[H]
InChI Identifier
InChI=1S/C48H49N13O9S6/c1-8-24(37(65)49-12-20(5)62)51-38(66)28-15-73-46(56-28)32-18-74-45(58-32)26-11-10-23-36(50-26)27-13-75-48(53-27)35(22(7)64)61-41(69)31-17-76-47(57-31)33(19(3)4)59-39(67)30-16-72-44(55-30)25(9-2)52-42(70)34(21(6)63)60-40(68)29-14-71-43(23)54-29/h8-11,13-22,33-35,62-64H,12H2,1-7H3,(H,49,65)(H,51,66)(H,52,70)(H,59,67)(H,60,68)(H,61,69)/b24-8-,25-9-/t20-,21-,22-,33+,34+,35-/m1/s1
InChI KeyMQGFYNRGFWXAKA-SRPYWAJFSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 100 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 200 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 300 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 400 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 600 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 700 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 800 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 900 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 1000 MHz, DMSO-d6, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of Origin
Species NameSourceReference
Bacterium; sewage; soilJEOL database
    • Fenet B., et al, Tetrahedron Lett. 43, 2367 (2002)
sewageJEOL database
    • Fenet B., et al, Tetrahedron Lett. 43, 2367 (2002)
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
logP4.23ALOGPS
logP3.91ChemAxon
logS-5.2ALOGPS
pKa (Strongest Acidic)11.93ChemAxon
pKa (Strongest Basic)-1.5ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area325.52 ŲChemAxon
Rotatable Bond Count10ChemAxon
Refractivity316.17 m³·mol⁻¹ChemAxon
Polarizability118.26 ųChemAxon
Number of Rings8ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID4445279  
KEGG Compound IDC12051  
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5282052  
PDB IDNot Available
ChEBI ID29631  
Good Scents IDNot Available
References
General References
  1. Ciufolini MA, Lefranc D: Micrococcin P1: structure, biology and synthesis. Nat Prod Rep. 2010 Mar;27(3):330-42. doi: 10.1039/b919071f. Epub 2010 Jan 22. [PubMed:20179875  ] 
  2. Bernard Fenet, Fabrice Pierre, Eric Cundliffe, Marco A.Ciufolini (2002). Bernard Fenet, Fabrice Pierre, Eric Cundliffe, Marco A.Ciufolini. The constitution of micrococcin P1: the Bycroft–Gowland hypothesis confirmed. Tetrahedron Letters, 43(13), 2367-2370, March 2002. Tetrahedron Letters. 
  3. JEOL [Link]