Np mrd loader

Showing NP-Card for 3-Deazauridine (NP0002880)

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Record Information
Version2.0
Created at2020-11-23 19:42:41 UTC
Updated at2021-08-12 19:52:24 UTC
NP-MRD IDNP0002880
Secondary Accession NumbersNone
Natural Product Identification
Common Name3-Deazauridine
Provided ByBMRBBMRB logo
Description1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyridine-2,4-dione 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). Based on a literature review very few articles have been published on 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyridine-2,4-dione.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002880 (3-Deazauridine)


     RDKit          2D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.5438   -1.1009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1510   -0.5441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9724   -1.4719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5795   -0.9152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3653    0.5695    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0275    1.1262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2742    1.9604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4528    1.0326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7985    0.3701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1443   -0.2925    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9346   -0.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7203   -1.8597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4357   -0.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0425   -0.5722    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5439    1.4973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3297    2.9819    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9367    0.9405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1866   -2.9566    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4009   -1.8430    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6718    2.4532    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2524    2.3017    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3050   -1.0464    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4611    1.7158    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3909    0.5417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3329   -0.9178    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8989   -2.7875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5348   -1.8139    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5607   -1.9798    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2432    2.4089    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4360    0.8937    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  6
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  1
 17 30  1  0
M  END
Download

3D MOL for NP0002880 (3-Deazauridine)

NP0002880
     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.3392   -0.0775   -0.0549 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0923    0.0186    0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612   -0.9722    0.6654 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9406   -0.9954    0.6075 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2433   -0.0071   -0.1065 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1722    0.0754   -0.2419 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8307    0.2226    0.9975 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1507    0.2606    0.5508 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1330    0.3267    1.6889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8338    1.5107    2.4016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2527   -0.9940   -0.2586 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1560   -0.7685   -1.2967 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8289   -1.1558   -0.7868 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8453   -1.0562   -2.1928 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0162    1.0072   -0.7561 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451    1.7977   -1.5851 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4519    1.2172   -0.5397 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7620   -1.7645    1.2346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3736   -1.7660    1.1021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4969    0.9405   -0.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.1313   -0.1282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1705    0.3980    1.3705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9743   -0.4949    2.4038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8345    2.3012    1.8097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5527   -1.8670    0.3543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7404   -0.7173   -2.1753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3708   -2.0908   -0.4735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118   -0.1021   -2.4271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5460    2.1010    0.1567 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9088    1.5206   -1.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  6
 14 28  1  0
 17 29  1  0
 17 30  1  0
M  END
Download

3D SDF for NP0002880 (3-Deazauridine)


     RDKit          2D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.5438   -1.1009    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1510   -0.5441    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9724   -1.4719    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5795   -0.9152    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3653    0.5695    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0275    1.1262    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2742    1.9604    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4528    1.0326    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7985    0.3701    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1443   -0.2925    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9346   -0.3750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7203   -1.8597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4357   -0.3172    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0425   -0.5722    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5439    1.4973    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3297    2.9819    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9367    0.9405    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1866   -2.9566    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4009   -1.8430    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6718    2.4532    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2524    2.3017    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3050   -1.0464    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4611    1.7158    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3909    0.5417    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3329   -0.9178    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8989   -2.7875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5348   -1.8139    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5607   -1.9798    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2432    2.4089    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4360    0.8937    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  6
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  1
 14 28  1  0
 17 29  1  1
 17 30  1  0
M  END
> <DATABASE_ID>
NP0002880

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@]1(CO)O[C@@]([H])(N2C=CC(=O)CC2=O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C10H13NO6/c12-4-6-8(15)9(16)10(17-6)11-2-1-5(13)3-7(11)14/h1-2,6,8-10,12,15-16H,3-4H2/t6-,8-,9-,10-/m1/s1

> <INCHI_KEY>
WIRVQQCUKDPURA-PEBGCTIMSA-N

> <FORMULA>
C10H13NO6

> <MOLECULAR_WEIGHT>
243.2133

> <EXACT_MASS>
243.074287153

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
22.690268259286412

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyridine-2,4-dione

> <ALOGPS_LOGP>
-1.82

> <JCHEM_LOGP>
-1.9905509449999998

> <ALOGPS_LOGS>
0.09

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.557420990320814

> <JCHEM_PKA_STRONGEST_ACIDIC>
7.560132610218339

> <JCHEM_PKA_STRONGEST_BASIC>
-2.980299138308136

> <JCHEM_POLAR_SURFACE_AREA>
107.30000000000001

> <JCHEM_REFRACTIVITY>
54.218199999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.02e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-pyridine-2,4-dione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for NP0002880 (3-Deazauridine)

NP0002880
     RDKit          3D

 30 31  0  0  0  0  0  0  0  0999 V2000
    5.3392   -0.0775   -0.0549 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0923    0.0186    0.0352 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2612   -0.9722    0.6654 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9406   -0.9954    0.6075 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2433   -0.0071   -0.1065 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1722    0.0754   -0.2419 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.8307    0.2226    0.9975 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1507    0.2606    0.5508 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1330    0.3267    1.6889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8338    1.5107    2.4016 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2527   -0.9940   -0.2586 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.1560   -0.7685   -1.2967 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8289   -1.1558   -0.7868 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.8453   -1.0562   -2.1928 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0162    1.0072   -0.7561 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4451    1.7977   -1.5851 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4519    1.2172   -0.5397 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7620   -1.7645    1.2346 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3736   -1.7660    1.1021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4969    0.9405   -0.8509 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2248    1.1313   -0.1282 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1705    0.3980    1.3705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9743   -0.4949    2.4038 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8345    2.3012    1.8097 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5527   -1.8670    0.3543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7404   -0.7173   -2.1753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3708   -2.0908   -0.4735 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118   -0.1021   -2.4271 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5460    2.1010    0.1567 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9088    1.5206   -1.5042 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
  8 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
  5 15  1  0
 15 16  2  0
 15 17  1  0
 17  2  1  0
 13  6  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  6
  8 21  1  6
  9 22  1  0
  9 23  1  0
 10 24  1  0
 11 25  1  1
 12 26  1  0
 13 27  1  6
 14 28  1  0
 17 29  1  0
 17 30  1  0
M  END
Download

PDB for NP0002880 (3-Deazauridine)

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   18  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    2    5                                                       
CONECT    2    1   11                                                       
CONECT    3    5    7                                                       
CONECT    4    6   12                                                       
CONECT    5    1    3   13                                                  
CONECT    6    4    8   17   18                                             
CONECT    7    3   11   14                                                  
CONECT    8    6    9   15   19                                             
CONECT    9    8   10   16   20                                             
CONECT   10    9   11   17   21                                             
CONECT   11    2    7   10                                                  
CONECT   12    4                                                            
CONECT   13    5                                                            
CONECT   14    7                                                            
CONECT   15    8                                                            
CONECT   16    9                                                            
CONECT   17    6   10                                                       
CONECT   18    6                                                            
CONECT   19    8                                                            
CONECT   20    9                                                            
CONECT   21   10                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   44    0
END
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3D PDB for NP0002880 (3-Deazauridine)

COMPND    NP0002880
HETATM    1  O1  UNL     1       5.339  -0.077  -0.055  1.00  0.00           O  
HETATM    2  C1  UNL     1       4.092   0.019   0.035  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.261  -0.972   0.665  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.941  -0.995   0.607  1.00  0.00           C  
HETATM    5  N1  UNL     1       1.243  -0.007  -0.107  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.172   0.075  -0.242  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.831   0.223   0.997  1.00  0.00           O  
HETATM    8  C5  UNL     1      -2.151   0.261   0.551  1.00  0.00           C  
HETATM    9  C6  UNL     1      -3.133   0.327   1.689  1.00  0.00           C  
HETATM   10  O3  UNL     1      -2.834   1.511   2.402  1.00  0.00           O  
HETATM   11  C7  UNL     1      -2.253  -0.994  -0.259  1.00  0.00           C  
HETATM   12  O4  UNL     1      -3.156  -0.769  -1.297  1.00  0.00           O  
HETATM   13  C8  UNL     1      -0.829  -1.156  -0.787  1.00  0.00           C  
HETATM   14  O5  UNL     1      -0.845  -1.056  -2.193  1.00  0.00           O  
HETATM   15  C9  UNL     1       2.016   1.007  -0.756  1.00  0.00           C  
HETATM   16  O6  UNL     1       1.445   1.798  -1.585  1.00  0.00           O  
HETATM   17  C10 UNL     1       3.452   1.217  -0.540  1.00  0.00           C  
HETATM   18  H1  UNL     1       3.762  -1.765   1.235  1.00  0.00           H  
HETATM   19  H2  UNL     1       1.374  -1.766   1.102  1.00  0.00           H  
HETATM   20  H3  UNL     1      -0.497   0.940  -0.851  1.00  0.00           H  
HETATM   21  H4  UNL     1      -2.225   1.131  -0.128  1.00  0.00           H  
HETATM   22  H5  UNL     1      -4.171   0.398   1.371  1.00  0.00           H  
HETATM   23  H6  UNL     1      -2.974  -0.495   2.404  1.00  0.00           H  
HETATM   24  H7  UNL     1      -2.835   2.301   1.810  1.00  0.00           H  
HETATM   25  H8  UNL     1      -2.553  -1.867   0.354  1.00  0.00           H  
HETATM   26  H9  UNL     1      -2.740  -0.717  -2.175  1.00  0.00           H  
HETATM   27  H10 UNL     1      -0.371  -2.091  -0.473  1.00  0.00           H  
HETATM   28  H11 UNL     1      -0.812  -0.102  -2.427  1.00  0.00           H  
HETATM   29  H12 UNL     1       3.546   2.101   0.157  1.00  0.00           H  
HETATM   30  H13 UNL     1       3.909   1.521  -1.504  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   17
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6   15
CONECT    6    7   13   20
CONECT    7    8
CONECT    8    9   11   21
CONECT    9   10   22   23
CONECT   10   24
CONECT   11   12   13   25
CONECT   12   26
CONECT   13   14   27
CONECT   14   28
CONECT   15   16   16   17
CONECT   17   29   30
END
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SMILES for NP0002880 (3-Deazauridine)

[H][C@]1(CO)O[C@@]([H])(N2C=CC(=O)CC2=O)[C@]([H])(O)[C@]1([H])O
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INCHI for NP0002880 (3-Deazauridine)

InChI=1S/C10H13NO6/c12-4-6-8(15)9(16)10(17-6)11-2-1-5(13)3-7(11)14/h1-2,6,8-10,12,15-16H,3-4H2/t6-,8-,9-,10-/m1/s1
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View in JSmol
SynonymsNot Available
Chemical FormulaC10H13NO6
Average Mass243.2133 Da
Monoisotopic Mass243.07429 Da
IUPAC Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyridine-2,4-dione
Traditional Name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3H-pyridine-2,4-dione
CAS Registry NumberNot Available
SMILES
[H][C@]1(CO)O[C@@]([H])(N2C=CC(=O)CC2=O)[C@]([H])(O)[C@]1([H])O
InChI Identifier
InChI=1S/C10H13NO6/c12-4-6-8(15)9(16)10(17-6)11-2-1-5(13)3-7(11)14/h1-2,6,8-10,12,15-16H,3-4H2/t6-,8-,9-,10-/m1/s1
InChI KeyWIRVQQCUKDPURA-PEBGCTIMSA-N
Experimental Spectra
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, simulated)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, experimental)Wishart LabWishart LabDavid Wishart2021-06-20View Spectrum
Predicted Spectra
Not Available
Chemical Shift Submissions
Not Available
Species
Species of OriginNot Available
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).
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentGlycosylamines
Alternative Parents
Substituents
  • N-glycosyl compound
  • Pentose monosaccharide
  • Tetrahydropyridine
  • Hydropyridine
  • Monosaccharide
  • 1,3-dicarbonyl compound
  • Oxolane
  • Tertiary carboxylic acid amide
  • Vinylogous amide
  • Cyclic ketone
  • Carboxamide group
  • Secondary alcohol
  • Ketone
  • Lactam
  • Azacycle
  • Organoheterocyclic compound
  • Carboxylic acid derivative
  • Oxacycle
  • Primary alcohol
  • Organic oxide
  • Organic nitrogen compound
  • Carbonyl group
  • Hydrocarbon derivative
  • Organonitrogen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.8ALOGPS
logP-2ChemAxon
logS0.09ALOGPS
pKa (Strongest Acidic)7.56ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area107.3 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity54.22 m³·mol⁻¹ChemAxon
Polarizability22.69 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDNot Available
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID2272346
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound3000824
PDB IDURD
ChEBI IDNot Available
Good Scents IDNot Available
References
General References