NP-MRD: Showing NP-Card for (4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid (NP0247460)

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Record Information

Version

2.0

Created at

2022-09-07 09:19:15 UTC

Updated at

2022-09-07 09:19:15 UTC

NP-MRD ID

NP0247460

Secondary Accession Numbers

None

Natural Product Identification

Common Name

(4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid

Description

A-500359 H belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether). (4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid is found in Streptomyces griseus. (4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid was first documented in 2003 (PMID: 12760682). Based on a literature review very few articles have been published on A-500359 H.

Structure

MOL 3D MOL SDF PDB SMILES InChI


  Mrv1652309072211192D          

 31 33  0  0  1  0            999 V2000
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  1  0  0  0
 17  4  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 25 26  1  0  0  0  0
 20 26  1  0  0  0  0
 26 27  2  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  6  0  0  0
M  END

     RDKit          3D

 50 52  0  0  0  0  0  0  0  0999 V2000
   -0.4489   -0.7768    4.0210 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8714   -1.6815    3.6913 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0047   -1.9805    2.4433 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5784   -3.2072    2.1427 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5599   -1.0455    1.3510 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.6653   -0.8338    0.5286 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9776    0.5207    0.4266 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.8621    0.8797   -0.9298 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8803    1.3636   -1.7271 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9228    1.1742   -3.1656 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0228    0.5513   -3.7679 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9771    1.6910   -3.8870 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8547    2.0317   -1.1168 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7581    2.1940    0.3563 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.7797    3.0969    0.7309 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3570    0.8298    0.9340 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.3868    0.9574    2.3155 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4827   -1.7747    0.5384 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.8878   -1.0714   -0.5702 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1643   -1.4416   -0.9028 C   0  0  1  0  0  0  0  0  0  0  0  0
    2.9468   -0.2775   -1.2813 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.5078    0.9264   -0.8867 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2220    2.0570   -1.2253 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3708    1.8677   -1.9673 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1017    3.0077   -2.3156 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7694    0.6341   -2.3394 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.0659   -0.4627   -2.0041 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4361   -1.6232   -2.3512 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7694   -2.1675    0.2695 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8052   -3.5526    0.0631 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7520   -1.8375    1.3704 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.7135   -2.8066    2.3431 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1553   -3.3002    1.3280 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1555   -0.1191    1.7530 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2626    1.1344    1.0341 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8958    1.3036   -3.9398 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6636    2.4216   -1.7134 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7648    2.4627    0.7544 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6958    3.7911    0.0112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1150    0.1155    0.5676 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5071    0.7900    2.7314 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1807   -2.7869    0.2719 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1427   -2.1110   -1.7790 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5909    1.0488   -0.2974 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9086    3.0573   -0.9298 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6400    3.9108   -2.3786 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7286   -1.7665    0.5928 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5267   -3.7512   -0.8459 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0190   -0.8287    1.7452 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3902   -2.6147    3.0177 H   0  0  0  0  0  0  0  0  0  0  0  0
 32 31  1  0
 31 29  1  0
 29 30  1  0
 29 20  1  0
 20 19  1  0
 19 18  1  0
 18  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 13  2  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
  9 10  1  0
 10 12  1  0
 10 11  2  0
  5  3  1  0
  3  4  1  0
  3  2  2  0
 20 21  1  0
 21 22  1  0
 22 23  2  0
 23 24  1  0
 24 25  1  0
 24 26  2  0
 26 27  1  0
 27 28  2  0
 18 31  1  0
 16  7  1  0
 27 21  1  0
 32 50  1  0
 31 49  1  1
 29 47  1  1
 30 48  1  0
 20 43  1  6
 18 42  1  6
  5 34  1  1
  7 35  1  1
 13 37  1  0
 14 38  1  1
 15 39  1  0
 16 40  1  1
 17 41  1  0
 12 36  1  0
  4 33  1  0
  2  1  1  0
 22 44  1  0
 23 45  1  0
 25 46  1  0
M  END


  Mrv1652309072211192D          

 31 33  0  0  1  0            999 V2000
    2.1434   -0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0000   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -1.2375    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.3819   -1.7224    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1270   -2.5070    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.6119   -3.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.4324   -3.0882    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9173   -3.7557    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5817   -4.5094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0667   -5.1768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7613   -4.5956    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2763   -3.9282    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4559   -4.0144    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -2.5070    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1830   -3.1745    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0470   -1.7224    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.7376   -1.4675    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  1  0  0  0
  6  5  1  6  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
  8 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  1  0  0  0
 13 15  1  0  0  0  0
  6 15  1  0  0  0  0
 15 16  1  1  0  0  0
 17  4  1  1  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  1  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 22 23  1  0  0  0  0
 23 24  1  0  0  0  0
 23 25  2  0  0  0  0
 25 26  1  0  0  0  0
 20 26  1  0  0  0  0
 26 27  2  0  0  0  0
 19 28  1  0  0  0  0
 28 29  1  6  0  0  0
 28 30  1  0  0  0  0
 17 30  1  0  0  0  0
 30 31  1  6  0  0  0
M  END
> <DATABASE_ID>
NP0247460

> <DATABASE_NAME>
NP-MRD

> <SMILES>
O[C@H]1[C@@H](O)[C@@H](O[C@@H]1[C@@H](O[C@H]1OC(=C[C@H](O)[C@@H]1O)C(O)=O)C(O)=N)N1C=CC(O)=NC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C16H19N3O12/c17-12(25)11(31-15-7(22)4(20)3-5(29-15)14(26)27)10-8(23)9(24)13(30-10)19-2-1-6(21)18-16(19)28/h1-4,7-11,13,15,20,22-24H,(H2,17,25)(H,26,27)(H,18,21,28)/t4-,7-,8-,9+,10-,11+,13+,15+/m0/s1

> <INCHI_KEY>
IHFPUFPCUYMJRS-IUKZBKQISA-N

> <FORMULA>
C16H19N3O12

> <MOLECULAR_WEIGHT>
445.337

> <EXACT_MASS>
445.096873064

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
37.93749959465815

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S,3S,4S)-2-[(R)-[(2S,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl](C-hydroxycarbonimidoyl)methoxy]-3,4-dihydroxy-3,4-dihydro-2H-pyran-6-carboxylic acid

> <JCHEM_LOGP>
-5.702045978061626

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
3.1593649209210173

> <JCHEM_PKA_STRONGEST_ACIDIC>
-3.8894091539733653

> <JCHEM_PKA_STRONGEST_BASIC>
11.691491001907307

> <JCHEM_POLAR_SURFACE_AREA>
242.89

> <JCHEM_REFRACTIVITY>
104.1177

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(4S,5S,6S)-6-[(R)-[(2S,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](C-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4H-pyran-2-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 07-SEP-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-SEP-22         0                                  
HETATM    1  N   UNK     0       4.001  -0.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0       2.667  -0.000   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0       0.000  -0.000   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM    8  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM   12  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0      -2.667   4.620   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       2.580  -3.215   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       2.104  -4.680   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       3.009  -5.926   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0       4.540  -5.765   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       5.446  -7.011   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       4.819  -8.417   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0       5.724  -9.663   0.000  0.00  0.00           O+0
HETATM   25  N   UNK     0       3.288  -8.578   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       2.382  -7.333   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0       0.851  -7.494   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       0.564  -4.680   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -0.342  -5.926   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       0.088  -3.215   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -1.377  -2.739   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   17                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7   15                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   12                                                  
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    8   13                                                       
CONECT   13   12   14   15                                                  
CONECT   14   13                                                            
CONECT   15   13    6   16                                                  
CONECT   16   15                                                            
CONECT   17    4   18   30                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   28                                                  
CONECT   20   19   21   26                                                  
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24   25                                                  
CONECT   24   23                                                            
CONECT   25   23   26                                                       
CONECT   26   25   20   27                                                  
CONECT   27   26                                                            
CONECT   28   19   29   30                                                  
CONECT   29   28                                                            
CONECT   30   28   17   31                                                  
CONECT   31   30                                                            
MASTER        0    0    0    0    0    0    0    0   31    0   66    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₆H₁₉N₃O₁₂

Average Mass

445.3370 Da

Monoisotopic Mass

445.09687 Da

IUPAC Name

(2S,3S,4S)-2-[(R)-[(2S,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxo-1,2-dihydropyrimidin-1-yl)oxolan-2-yl](C-hydroxycarbonimidoyl)methoxy]-3,4-dihydroxy-3,4-dihydro-2H-pyran-6-carboxylic acid

Traditional Name

(4S,5S,6S)-6-[(R)-[(2S,3S,4R,5R)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](C-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4H-pyran-2-carboxylic acid

CAS Registry Number

Not Available

SMILES

O[C@H]1[C@@H](O)[C@@H](O[C@@H]1[C@@H](O[C@H]1OC(=C[C@H](O)[C@@H]1O)C(O)=O)C(O)=N)N1C=CC(O)=NC1=O

InChI Identifier

InChI=1S/C16H19N3O12/c17-12(25)11(31-15-7(22)4(20)3-5(29-15)14(26)27)10-8(23)9(24)13(30-10)19-2-1-6(21)18-16(19)28/h1-4,7-11,13,15,20,22-24H,(H2,17,25)(H,26,27)(H,18,21,28)/t4-,7-,8-,9+,10-,11+,13+,15+/m0/s1

InChI Key

IHFPUFPCUYMJRS-IUKZBKQISA-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, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, H₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, 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 griseus	LOTUS Database	35616633

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycosylamines. Glycosylamines are compounds consisting of an amine with a beta-N-glycosidic bond to a carbohydrate, thus forming a cyclic hemiaminal ether bond (alpha-amino ether).

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Glycosylamines

Alternative Parents

Substituents

Disaccharide
N-glycosyl compound
Pyrimidone
Hydropyrimidine
Pyrimidine
Oxolane
Heteroaromatic compound
Vinylogous amide
Carboxamide group
Lactam
Primary carboxylic acid amide
Secondary alcohol
Urea
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Oxacycle
Azacycle
Acetal
Organoheterocyclic compound
Hydrocarbon derivative
Organonitrogen compound
Alcohol
Organic oxide
Organopnictogen compound
Organic nitrogen compound
Carbonyl group
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

Not Available

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	-5.7	ChemAxon
pKa (Strongest Acidic)	-3.9	ChemAxon
pKa (Strongest Basic)	11.69	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	8	ChemAxon
Polar Surface Area	242.89 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	104.12 m³·mol⁻¹	ChemAxon
Polarizability	37.94 Å³	ChemAxon
Number of Rings	3	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

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

2276151

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

3006191

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Muramatsu Y, Miyakoshi S, Ogawa Y, Ohnuki T, Ishii MM, Arai M, Takatsu T, Inukai M: Studies on novel bacterial translocase I inhibitors, A-500359s. III. Deaminocaprolactam derivatives of capuramycin: A-500359 E, F, H; M-1 and M-2. J Antibiot (Tokyo). 2003 Mar;56(3):259-67. doi: 10.7164/antibiotics.56.259. [PubMed:12760682 ]
LOTUS database [Link]

Showing NP-Card for (4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid (NP0247460)

MOL for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

3D MOL for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

3D SDF for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

3D-SDF for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

PDB for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

3D PDB for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

SMILES for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

INCHI for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

Structure for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)

3D Structure for NP0247460 ((4s,5s,6s)-6-[(r)-[(2s,3s,4r,5r)-3,4-dihydroxy-5-(4-hydroxy-2-oxopyrimidin-1-yl)oxolan-2-yl](c-hydroxycarbonimidoyl)methoxy]-4,5-dihydroxy-5,6-dihydro-4h-pyran-2-carboxylic acid)