NP-MRD: Showing NP-Card for SB-217452 (NP0003613)

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Record Information

Version

2.0

Created at

2020-12-09 00:48:50 UTC

Updated at

2021-07-15 16:46:53 UTC

NP-MRD ID

NP0003613

Secondary Accession Numbers

None

Natural Product Identification

Common Name

SB-217452

Provided By

NPAtlas

Description

SB-217452 is found in Streptomyces sp. and Streptomyces sp. ATCC 700974. SB-217452 was first documented in 2000 (PMID: 11217799). Based on a literature review very few articles have been published on (2R,3S)-2-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-3-[(2S,3R,4R,5R)-3,4-dihydroxy-5-{4-[(C-hydroxycarbonimidoyl)imino]-3-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-1-yl}thiolan-2-yl]-3-hydroxypropanoic acid.

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242117483D          

 56 57  0  0  0  0            999 V2000
   -6.0497    2.7262    0.4597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2272    1.5929    0.0481 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6902    0.6462   -0.7867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9038    0.7404   -1.2414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4553   -0.2195   -2.1225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1134   -1.3580   -1.6218 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3587   -0.0563   -3.3518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9339   -0.4286   -1.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6353   -0.5261   -0.7001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1688    0.4131    0.1310 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8253    0.3768    0.6784 C   0  0  2  0  0  0  0  0  0  0  0  0
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    5.1093   -0.3425   -1.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9089   -1.4893   -1.6676 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.3298    1.7382   -1.0510 N   0  0  1  0  0  0  0  0  0  0  0  0
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   -3.5028    2.3290    1.2788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0731    2.3833    0.7530 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.1320   -1.5088   -1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
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  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
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M  END

     RDKit          3D

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   -4.9339   -0.4286   -1.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6353   -0.5261   -0.7001 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END


  Mrv1652306242117483D          

 56 57  0  0  0  0            999 V2000
   -6.0497    2.7262    0.4597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2272    1.5929    0.0481 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.0571    3.5294   -0.2909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1320   -1.5088   -1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5880   -2.0883   -1.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3018   -1.2038   -1.8674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705   -1.3455   -0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6325    1.1788    1.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6833   -1.8089   -0.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0120    0.3661   -0.7892 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7102    1.1829    1.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259   -1.7289   -0.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4022    0.9584    0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0027    0.6313   -2.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9517    1.6270   -0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7544    2.3931   -1.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5441   -1.2315   -2.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8185   -0.3682   -0.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5479    1.4239   -1.7819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1191   -3.2487    1.8173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.1702    2.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2264   -1.5734    3.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6544   -1.8058    0.6695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8635   -0.4025    2.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  2  0  0  0  0
  3  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 18 20  1  0  0  0  0
 20 21  1  0  0  0  0
 20 22  1  0  0  0  0
 22 23  1  0  0  0  0
 16 24  1  0  0  0  0
 24 25  2  0  0  0  0
 24 26  1  0  0  0  0
 13 27  1  0  0  0  0
 27 28  1  0  0  0  0
 27 29  1  0  0  0  0
 29 30  1  0  0  0  0
 10 31  1  0  0  0  0
 31 32  2  0  0  0  0
 31  2  1  0  0  0  0
 29 11  1  0  0  0  0
  1 33  1  0  0  0  0
  1 34  1  0  0  0  0
  1 35  1  0  0  0  0
  6 36  1  0  0  0  0
  6 37  1  0  0  0  0
  8 38  1  0  0  0  0
  9 39  1  0  0  0  0
 11 40  1  1  0  0  0
 13 41  1  6  0  0  0
 14 42  1  6  0  0  0
 15 43  1  0  0  0  0
 16 44  1  6  0  0  0
 17 45  1  0  0  0  0
 20 46  1  6  0  0  0
 21 47  1  0  0  0  0
 21 48  1  0  0  0  0
 22 49  1  0  0  0  0
 22 50  1  0  0  0  0
 23 51  1  0  0  0  0
 26 52  1  0  0  0  0
 27 53  1  1  0  0  0
 28 54  1  0  0  0  0
 29 55  1  6  0  0  0
 30 56  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0003613

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)[C@]([H])(N([H])C(=O)[C@@]([H])(N([H])[H])C([H])([H])O[H])[C@]([H])(O[H])[C@]1([H])S[C@@]([H])(N2C([H])=C([H])\C(=N/C(=O)N([H])[H])N(C2=O)C([H])([H])[H])[C@]([H])(O[H])[C@@]1([H])O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C16H24N6O9S/c1-21-6(19-15(18)30)2-3-22(16(21)31)13-10(26)9(25)11(32-13)8(24)7(14(28)29)20-12(27)5(17)4-23/h2-3,5,7-11,13,23-26H,4,17H2,1H3,(H2,18,30)(H,20,27)(H,28,29)/b19-6+/t5-,7+,8-,9+,10+,11-,13+/m0/s1

> <INCHI_KEY>
NGJDTPRGDCKRHD-ZAUJBZHMSA-N

> <FORMULA>
C16H24N6O9S

> <MOLECULAR_WEIGHT>
476.46

> <EXACT_MASS>
476.132547551

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
56

> <JCHEM_AVERAGE_POLARIZABILITY>
45.30118564710885

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-[(2S,3R,4R,5R)-5-[(4E)-4-(carbamoylimino)-3-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-1-yl]-3,4-dihydroxythiolan-2-yl]-3-hydroxypropanoic acid

> <ALOGPS_LOGP>
-2.22

> <JCHEM_LOGP>
-7.201130321082813

> <ALOGPS_LOGS>
-2.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.185615023353732

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.2008639363888256

> <JCHEM_PKA_STRONGEST_BASIC>
7.849238744902292

> <JCHEM_POLAR_SURFACE_AREA>
252.33999999999995

> <JCHEM_REFRACTIVITY>
106.20379999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.59e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R,3S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-[(2S,3R,4R,5R)-5-[(4E)-4-(carbamoylimino)-3-methyl-2-oxopyrimidin-1-yl]-3,4-dihydroxythiolan-2-yl]-3-hydroxypropanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$

     RDKit          3D

 56 57  0  0  0  0  0  0  0  0999 V2000
   -6.0497    2.7262    0.4597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2272    1.5929    0.0481 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6902    0.6462   -0.7867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9038    0.7404   -1.2414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4553   -0.2195   -2.1225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1134   -1.3580   -1.6218 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3587   -0.0563   -3.3518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9339   -0.4286   -1.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6353   -0.5261   -0.7001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1688    0.4131    0.1310 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8253    0.3768    0.6784 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5860    0.2657   -0.6395 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6296   -0.8298    0.2537 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9078   -0.0776    0.3232 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8751    1.1110    1.0308 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1882   -0.8073    0.4555 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2853    0.0466   -0.0839 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1093   -0.3425   -1.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9089   -1.4893   -1.6676 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2006    0.4526   -1.7111 C   0  0  1  0  0  0  0  0  0  0  0  0
    6.3298    1.7382   -1.0510 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5420   -0.2507   -1.6123 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5116    0.5255   -2.2394 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5587   -1.1956    1.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1898   -0.3370    2.5128 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2566   -2.4226    2.3853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0356   -0.8209    1.6197 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3619   -1.8683    2.4352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5379   -0.9387    1.3636 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1543   -1.1029    2.5742 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9501    1.4394    0.4891 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5028    2.3290    1.2788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0731    2.3833    0.7530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5745    3.1378    1.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0571    3.5294   -0.2909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1320   -1.5088   -1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5880   -2.0883   -1.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3018   -1.2038   -1.8674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705   -1.3455   -0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6325    1.1788    1.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6833   -1.8089   -0.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0120    0.3661   -0.7892 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7102    1.1829    1.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259   -1.7289   -0.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4022    0.9584    0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0027    0.6313   -2.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9517    1.6270   -0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7544    2.3931   -1.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5441   -1.2315   -2.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8185   -0.3682   -0.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5479    1.4239   -1.7819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1191   -3.2487    1.8173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.1702    2.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2264   -1.5734    3.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6544   -1.8058    0.6695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8635   -0.4025    2.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  3  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 16 24  1  0
 24 25  2  0
 24 26  1  0
 13 27  1  0
 27 28  1  0
 27 29  1  0
 29 30  1  0
 10 31  1  0
 31 32  2  0
 31  2  1  0
 29 11  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  6 36  1  0
  6 37  1  0
  8 38  1  0
  9 39  1  0
 11 40  1  1
 13 41  1  6
 14 42  1  6
 15 43  1  0
 16 44  1  6
 17 45  1  0
 20 46  1  6
 21 47  1  0
 21 48  1  0
 22 49  1  0
 22 50  1  0
 23 51  1  0
 26 52  1  0
 27 53  1  1
 28 54  1  0
 29 55  1  6
 30 56  1  0
M  END

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  C   UNK     0      -6.050   2.726   0.460  0.00  0.00           C+0
HETATM    2  N   UNK     0      -5.227   1.593   0.048  0.00  0.00           N+0
HETATM    3  C   UNK     0      -5.690   0.646  -0.787  0.00  0.00           C+0
HETATM    4  N   UNK     0      -6.904   0.740  -1.241  0.00  0.00           N+0
HETATM    5  C   UNK     0      -7.455  -0.220  -2.123  0.00  0.00           C+0
HETATM    6  N   UNK     0      -8.113  -1.358  -1.622  0.00  0.00           N+0
HETATM    7  O   UNK     0      -7.359  -0.056  -3.352  0.00  0.00           O+0
HETATM    8  C   UNK     0      -4.934  -0.429  -1.188  0.00  0.00           C+0
HETATM    9  C   UNK     0      -3.635  -0.526  -0.700  0.00  0.00           C+0
HETATM   10  N   UNK     0      -3.169   0.413   0.131  0.00  0.00           N+0
HETATM   11  C   UNK     0      -1.825   0.377   0.678  0.00  0.00           C+0
HETATM   12  S   UNK     0      -0.586   0.266  -0.640  0.00  0.00           S+0
HETATM   13  C   UNK     0       0.630  -0.830   0.254  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.908  -0.078   0.323  0.00  0.00           C+0
HETATM   15  O   UNK     0       1.875   1.111   1.031  0.00  0.00           O+0
HETATM   16  C   UNK     0       3.188  -0.807   0.456  0.00  0.00           C+0
HETATM   17  N   UNK     0       4.285   0.047  -0.084  0.00  0.00           N+0
HETATM   18  C   UNK     0       5.109  -0.343  -1.140  0.00  0.00           C+0
HETATM   19  O   UNK     0       4.909  -1.489  -1.668  0.00  0.00           O+0
HETATM   20  C   UNK     0       6.201   0.453  -1.711  0.00  0.00           C+0
HETATM   21  N   UNK     0       6.330   1.738  -1.051  0.00  0.00           N+0
HETATM   22  C   UNK     0       7.542  -0.251  -1.612  0.00  0.00           C+0
HETATM   23  O   UNK     0       8.512   0.526  -2.239  0.00  0.00           O+0
HETATM   24  C   UNK     0       3.559  -1.196   1.832  0.00  0.00           C+0
HETATM   25  O   UNK     0       4.190  -0.337   2.513  0.00  0.00           O+0
HETATM   26  O   UNK     0       3.257  -2.423   2.385  0.00  0.00           O+0
HETATM   27  C   UNK     0      -0.036  -0.821   1.620  0.00  0.00           C+0
HETATM   28  O   UNK     0       0.362  -1.868   2.435  0.00  0.00           O+0
HETATM   29  C   UNK     0      -1.538  -0.939   1.364  0.00  0.00           C+0
HETATM   30  O   UNK     0      -2.154  -1.103   2.574  0.00  0.00           O+0
HETATM   31  C   UNK     0      -3.950   1.439   0.489  0.00  0.00           C+0
HETATM   32  O   UNK     0      -3.503   2.329   1.279  0.00  0.00           O+0
HETATM   33  H   UNK     0      -7.073   2.383   0.753  0.00  0.00           H+0
HETATM   34  H   UNK     0      -5.574   3.138   1.380  0.00  0.00           H+0
HETATM   35  H   UNK     0      -6.057   3.529  -0.291  0.00  0.00           H+0
HETATM   36  H   UNK     0      -9.132  -1.509  -1.767  0.00  0.00           H+0
HETATM   37  H   UNK     0      -7.588  -2.088  -1.085  0.00  0.00           H+0
HETATM   38  H   UNK     0      -5.302  -1.204  -1.867  0.00  0.00           H+0
HETATM   39  H   UNK     0      -2.970  -1.345  -0.969  0.00  0.00           H+0
HETATM   40  H   UNK     0      -1.633   1.179   1.388  0.00  0.00           H+0
HETATM   41  H   UNK     0       0.683  -1.809  -0.203  0.00  0.00           H+0
HETATM   42  H   UNK     0       2.012   0.366  -0.789  0.00  0.00           H+0
HETATM   43  H   UNK     0       2.710   1.183   1.553  0.00  0.00           H+0
HETATM   44  H   UNK     0       3.226  -1.729  -0.156  0.00  0.00           H+0
HETATM   45  H   UNK     0       4.402   0.958   0.378  0.00  0.00           H+0
HETATM   46  H   UNK     0       6.003   0.631  -2.783  0.00  0.00           H+0
HETATM   47  H   UNK     0       6.952   1.627  -0.221  0.00  0.00           H+0
HETATM   48  H   UNK     0       6.754   2.393  -1.744  0.00  0.00           H+0
HETATM   49  H   UNK     0       7.544  -1.232  -2.126  0.00  0.00           H+0
HETATM   50  H   UNK     0       7.819  -0.368  -0.533  0.00  0.00           H+0
HETATM   51  H   UNK     0       8.548   1.424  -1.782  0.00  0.00           H+0
HETATM   52  H   UNK     0       3.119  -3.249   1.817  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.123   0.170   2.092  0.00  0.00           H+0
HETATM   54  H   UNK     0       0.226  -1.573   3.376  0.00  0.00           H+0
HETATM   55  H   UNK     0      -1.654  -1.806   0.670  0.00  0.00           H+0
HETATM   56  H   UNK     0      -2.864  -0.403   2.656  0.00  0.00           H+0
CONECT    1    2   33   34   35                                             
CONECT    2    1    3   31                                                  
CONECT    3    2    4    8                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6    7                                                  
CONECT    6    5   36   37                                                  
CONECT    7    5                                                            
CONECT    8    3    9   38                                                  
CONECT    9    8   10   39                                                  
CONECT   10    9   11   31                                                  
CONECT   11   10   12   29   40                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   27   41                                             
CONECT   14   13   15   16   42                                             
CONECT   15   14   43                                                       
CONECT   16   14   17   24   44                                             
CONECT   17   16   18   45                                                  
CONECT   18   17   19   20                                                  
CONECT   19   18                                                            
CONECT   20   18   21   22   46                                             
CONECT   21   20   47   48                                                  
CONECT   22   20   23   49   50                                             
CONECT   23   22   51                                                       
CONECT   24   16   25   26                                                  
CONECT   25   24                                                            
CONECT   26   24   52                                                       
CONECT   27   13   28   29   53                                             
CONECT   28   27   54                                                       
CONECT   29   27   30   11   55                                             
CONECT   30   29   56                                                       
CONECT   31   10   32    2                                                  
CONECT   32   31                                                            
CONECT   33    1                                                            
CONECT   34    1                                                            
CONECT   35    1                                                            
CONECT   36    6                                                            
CONECT   37    6                                                            
CONECT   38    8                                                            
CONECT   39    9                                                            
CONECT   40   11                                                            
CONECT   41   13                                                            
CONECT   42   14                                                            
CONECT   43   15                                                            
CONECT   44   16                                                            
CONECT   45   17                                                            
CONECT   46   20                                                            
CONECT   47   21                                                            
CONECT   48   21                                                            
CONECT   49   22                                                            
CONECT   50   22                                                            
CONECT   51   23                                                            
CONECT   52   26                                                            
CONECT   53   27                                                            
CONECT   54   28                                                            
CONECT   55   29                                                            
CONECT   56   30                                                            
MASTER        0    0    0    0    0    0    0    0   56    0  114    0
END

RDKit          3D

56 57  0  0  0  0  0  0  0  0999 V2000
   -6.0497    2.7262    0.4597 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2272    1.5929    0.0481 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6902    0.6462   -0.7867 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9038    0.7404   -1.2414 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4553   -0.2195   -2.1225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1134   -1.3580   -1.6218 N   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3587   -0.0563   -3.3518 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9339   -0.4286   -1.1880 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6353   -0.5261   -0.7001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1688    0.4131    0.1310 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8253    0.3768    0.6784 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5860    0.2657   -0.6395 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.6296   -0.8298    0.2537 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9078   -0.0776    0.3232 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.8751    1.1110    1.0308 O   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1093   -0.3425   -1.1401 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9089   -1.4893   -1.6676 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.3298    1.7382   -1.0510 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5420   -0.2507   -1.6123 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5116    0.5255   -2.2394 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5587   -1.1956    1.8323 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1898   -0.3370    2.5128 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2566   -2.4226    2.3853 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0356   -0.8209    1.6197 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3619   -1.8683    2.4352 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5379   -0.9387    1.3636 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1543   -1.1029    2.5742 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9501    1.4394    0.4891 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5028    2.3290    1.2788 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0731    2.3833    0.7530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5745    3.1378    1.3802 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0571    3.5294   -0.2909 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1320   -1.5088   -1.7669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5880   -2.0883   -1.0853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3018   -1.2038   -1.8674 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9705   -1.3455   -0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6325    1.1788    1.3876 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6833   -1.8089   -0.2026 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0120    0.3661   -0.7892 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7102    1.1829    1.5533 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2259   -1.7289   -0.1564 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4022    0.9584    0.3775 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0027    0.6313   -2.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9517    1.6270   -0.2214 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7544    2.3931   -1.7443 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5441   -1.2315   -2.1259 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8185   -0.3682   -0.5326 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.5479    1.4239   -1.7819 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1191   -3.2487    1.8173 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1226    0.1702    2.0916 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2264   -1.5734    3.3759 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6544   -1.8058    0.6695 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8635   -0.4025    2.6562 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  3  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 16 24  1  0
 24 25  2  0
 24 26  1  0
 13 27  1  0
 27 28  1  0
 27 29  1  0
 29 30  1  0
 10 31  1  0
 31 32  2  0
 31  2  1  0
 29 11  1  0
  1 33  1  0
  1 34  1  0
  1 35  1  0
  6 36  1  0
  6 37  1  0
  8 38  1  0
  9 39  1  0
 11 40  1  1
 13 41  1  6
 14 42  1  6
 15 43  1  0
 16 44  1  6
 17 45  1  0
 20 46  1  6
 21 47  1  0
 21 48  1  0
 22 49  1  0
 22 50  1  0
 23 51  1  0
 26 52  1  0
 27 53  1  1
 28 54  1  0
 29 55  1  6
 30 56  1  0
M  END

View in JSmol View NMR Assignments

Synonyms

Value	Source
(2R,3S)-2-{[(2S)-2-amino-1,3-dihydroxypropylidene]amino}-3-[(2S,3R,4R,5R)-3,4-dihydroxy-5-{4-[(C-hydroxycarbonimidoyl)imino]-3-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-1-yl}thiolan-2-yl]-3-hydroxypropanoate	Generator

Chemical Formula

C₁₆H₂₄N₆O₉S

Average Mass

476.4600 Da

Monoisotopic Mass

476.13255 Da

IUPAC Name

(2R,3S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-[(2S,3R,4R,5R)-5-[(4E)-4-(carbamoylimino)-3-methyl-2-oxo-1,2,3,4-tetrahydropyrimidin-1-yl]-3,4-dihydroxythiolan-2-yl]-3-hydroxypropanoic acid

Traditional Name

(2R,3S)-2-[(2S)-2-amino-3-hydroxypropanamido]-3-[(2S,3R,4R,5R)-5-[(4E)-4-(carbamoylimino)-3-methyl-2-oxopyrimidin-1-yl]-3,4-dihydroxythiolan-2-yl]-3-hydroxypropanoic acid

CAS Registry Number

Not Available

SMILES

CN1C(=O)N(C=CC1=NC(N)=O)[C@@H]1S[C@@H]([C@@H](O)[C@@H](NC(=O)[C@@H](N)CO)C(O)=O)[C@H](O)[C@H]1O

InChI Identifier

InChI=1S/C16H24N6O9S/c1-21-6(19-15(18)30)2-3-22(16(21)31)13-10(26)9(25)11(32-13)8(24)7(14(28)29)20-12(27)5(17)4-23/h2-3,5,7-11,13,23-26H,4,17H2,1H3,(H2,18,30)(H,20,27)(H,28,29)/t5-,7+,8-,9+,10+,11-,13+/m0/s1

InChI Key

NGJDTPRGDCKRHD-ZAUJBZHMSA-N

Experimental Spectra

Not Available

Predicted Spectra

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

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Streptomyces sp.	NPAtlas	11217799
Streptomyces sp. ATCC 700974	Bacteria	KNApSAcK

Chemical Taxonomy

Classification

Not classified

Physical Properties

State

Not Available

Experimental Properties

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

Predicted Properties

Property	Value	Source
logP	-2.2	ALOGPS
logP	-7.2	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	3.2	ChemAxon
pKa (Strongest Basic)	7.85	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	252.34 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	106.2 m³·mol⁻¹	ChemAxon
Polarizability	45.3 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA003591

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

78440083

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

139584089

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Stefanska AL, Fulston M, Houge-Frydrych CS, Jones JJ, Warr SR: A potent seryl tRNA synthetase inhibitor SB-217452 isolated from a Streptomyces species. J Antibiot (Tokyo). 2000 Dec;53(12):1346-53. doi: 10.7164/antibiotics.53.1346. [PubMed:11217799 ]

Showing NP-Card for SB-217452 (NP0003613)

MOL for NP0003613 (SB-217452)

3D MOL for NP0003613 (SB-217452)

3D SDF for NP0003613 (SB-217452)

3D-SDF for NP0003613 (SB-217452)

PDB for NP0003613 (SB-217452)

3D PDB for NP0003613 (SB-217452)

SMILES for NP0003613 (SB-217452)

INCHI for NP0003613 (SB-217452)

Structure for NP0003613 (SB-217452)

3D Structure for NP0003613 (SB-217452)