NP-MRD: Showing NP-Card for 2'-Deoxycytidine (NP0002699)

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Record Information

Version

1.0

Created at

2020-11-23 19:38:15 UTC

Updated at

2021-08-12 19:51:53 UTC

NP-MRD ID

NP0002699

Secondary Accession Numbers

None

Natural Product Identification

Common Name

2'-Deoxycytidine

Provided By

BMRB

Description

It was first documented in 2008 (PMID: 17984079). Based on a literature review very few articles have been published on 1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


     RDKit          2D

 29 30  0  0  0  0  0  0  0  0999 V2000
   -5.2307   -1.0508    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8291   -0.5164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5911    0.9646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1896    1.4990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0260    0.5524    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3756    1.0868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6355    1.9009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7990    0.9543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1340    0.2703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2583   -0.4449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0203   -1.9259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7824   -3.4069    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7606   -0.3630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2640   -0.9286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3284   -1.9019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6655   -1.4630    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4687   -2.5318    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3943   -0.1042    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7547    1.9112    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9516    2.9800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3024    2.4248    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6941    3.0687    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6985    2.9592    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6188    2.2104    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3939    1.0844    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7063   -0.8364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5013   -2.1639    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6713   -1.8758    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9459   -4.3535    0.0000 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
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  2  0
 13  6  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  1
  7 22  1  6
  7 23  1  0
  8 24  1  6
  9 25  1  0
 10 26  1  1
 11 27  1  6
 11 28  1  0
 12 29  1  0
M  END

NP0002699
     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
    5.0504    0.9901   -0.3086 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8442    0.6018   -0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6000   -0.3683    0.9254 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3152   -0.7634    1.2088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2900   -0.2014    0.5561 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0766   -0.5831    0.8190 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6608   -1.4125   -0.3240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1321   -1.1035   -0.2820 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8910   -2.1267    0.2474 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1805    0.0574    0.6919 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1504    1.0765    0.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2095    2.2058    0.9494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8994    0.5579    0.7905 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5201    0.7556   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4481    1.3320   -1.0538 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7802    1.1351   -0.6524 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1949    1.7129   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4373   -0.8132    1.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995   -1.5266    1.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1775   -1.1429    1.7658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2092   -1.0143   -1.2546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -2.4688   -0.2405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4880   -0.7854   -1.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4662   -3.0160    0.1831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5444   -0.2830    1.6877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1476    0.5810    0.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8265    1.3664   -0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6350    2.9343    0.5589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298    2.3024   -1.3185 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  1  0
 14 16  2  0
 16  2  1  0
 13  6  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  1
  7 21  1  0
  7 22  1  0
  8 23  1  6
  9 24  1  0
 10 25  1  1
 11 26  1  0
 11 27  1  0
 12 28  1  0
 15 29  1  0
M  END


     RDKit          2D

 29 30  0  0  0  0  0  0  0  0999 V2000
   -5.2307   -1.0508    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8291   -0.5164    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5911    0.9646    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1896    1.4990    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0260    0.5524    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.3756    1.0868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6355    1.9009    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7990    0.9543    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1340    0.2703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2583   -0.4449    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0203   -1.9259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7824   -3.4069    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7606   -0.3630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2640   -0.9286    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3284   -1.9019    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6655   -1.4630    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4687   -2.5318    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3943   -0.1042    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7547    1.9112    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9516    2.9800    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3024    2.4248    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6941    3.0687    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6985    2.9592    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6188    2.2104    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3939    1.0844    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7063   -0.8364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5013   -2.1639    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6713   -1.8758    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9459   -4.3535    0.0000 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
  6  7  1  0
  7  8  1  0
  8  9  1  0
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  2  0
 14 16  1  0
 16  2  2  0
 13  6  1  0
  1 17  1  0
  1 18  1  0
  3 19  1  0
  4 20  1  0
  6 21  1  1
  7 22  1  6
  7 23  1  0
  8 24  1  6
  9 25  1  0
 10 26  1  1
 11 27  1  6
 11 28  1  0
 12 29  1  0
M  END
> <DATABASE_ID>
NP0002699

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H][C@@]1(O)C[C@]([H])(O[C@@]1([H])CO)N1C=CC(=N)N=C1O

> <INCHI_IDENTIFIER>
InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m1/s1

> <INCHI_KEY>
CKTSBUTUHBMZGZ-CHKWXVPMSA-N

> <FORMULA>
C9H13N3O4

> <MOLECULAR_WEIGHT>
227.2172

> <EXACT_MASS>
227.090605919

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
21.819344005465798

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-0.9187417609999995

> <ALOGPS_LOGS>
-2.12

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
13.89571554273953

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.240943338330005

> <JCHEM_PKA_STRONGEST_BASIC>
2.5455694208970447

> <JCHEM_POLAR_SURFACE_AREA>
109.37000000000002

> <JCHEM_REFRACTIVITY>
64.4466

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.72e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-iminopyrimidin-2-ol

> <JCHEM_VEBER_RULE>
0

$$$$

NP0002699
     RDKit          3D

 29 30  0  0  0  0  0  0  0  0999 V2000
    5.0504    0.9901   -0.3086 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8442    0.6018   -0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6000   -0.3683    0.9254 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3152   -0.7634    1.2088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2900   -0.2014    0.5561 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0766   -0.5831    0.8190 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6608   -1.4125   -0.3240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1321   -1.1035   -0.2820 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8910   -2.1267    0.2474 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1805    0.0574    0.6919 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1504    1.0765    0.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2095    2.2058    0.9494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8994    0.5579    0.7905 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5201    0.7556   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4481    1.3320   -1.0538 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7802    1.1351   -0.6524 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1949    1.7129   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4373   -0.8132    1.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995   -1.5266    1.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1775   -1.1429    1.7658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2092   -1.0143   -1.2546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -2.4688   -0.2405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4880   -0.7854   -1.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4662   -3.0160    0.1831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5444   -0.2830    1.6877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1476    0.5810    0.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8265    1.3664   -0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6350    2.9343    0.5589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298    2.3024   -1.3185 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  1  0
 14 16  2  0
 16  2  1  0
 13  6  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  1
  7 21  1  0
  7 22  1  0
  8 23  1  6
  9 24  1  0
 10 25  1  1
 11 26  1  0
 11 27  1  0
 12 28  1  0
 15 29  1  0
M  END

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  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   11  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+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  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+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
CONECT    1    2    7                                                       
CONECT    2    1   12                                                       
CONECT    3    5    8                                                       
CONECT    4    6   13                                                       
CONECT    5    3    6   14   17                                             
CONECT    6    4    5   16   18                                             
CONECT    7    1   10   11                                                  
CONECT    8    3   12   16   19                                             
CONECT    9   11   12   15                                                  
CONECT   10    7                                                            
CONECT   11    7    9                                                       
CONECT   12    2    8    9                                                  
CONECT   13    4                                                            
CONECT   14    5                                                            
CONECT   15    9                                                            
CONECT   16    6    8                                                       
CONECT   17    5                                                            
CONECT   18    6                                                            
CONECT   19    8                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   40    0
END

COMPND    NP0002699
HETATM    1  N1  UNL     1       5.050   0.990  -0.309  1.00  0.00           N  
HETATM    2  C1  UNL     1       3.844   0.602  -0.025  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.600  -0.368   0.925  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.315  -0.763   1.209  1.00  0.00           C  
HETATM    5  N2  UNL     1       1.290  -0.201   0.556  1.00  0.00           N  
HETATM    6  C4  UNL     1      -0.077  -0.583   0.819  1.00  0.00           C  
HETATM    7  C5  UNL     1      -0.661  -1.413  -0.324  1.00  0.00           C  
HETATM    8  C6  UNL     1      -2.132  -1.104  -0.282  1.00  0.00           C  
HETATM    9  O1  UNL     1      -2.891  -2.127   0.247  1.00  0.00           O  
HETATM   10  C7  UNL     1      -2.181   0.057   0.692  1.00  0.00           C  
HETATM   11  C8  UNL     1      -3.150   1.076   0.136  1.00  0.00           C  
HETATM   12  O2  UNL     1      -3.209   2.206   0.949  1.00  0.00           O  
HETATM   13  O3  UNL     1      -0.899   0.558   0.790  1.00  0.00           O  
HETATM   14  C9  UNL     1       1.520   0.756  -0.383  1.00  0.00           C  
HETATM   15  O4  UNL     1       0.448   1.332  -1.054  1.00  0.00           O  
HETATM   16  N3  UNL     1       2.780   1.135  -0.652  1.00  0.00           N  
HETATM   17  H1  UNL     1       5.195   1.713  -1.020  1.00  0.00           H  
HETATM   18  H2  UNL     1       4.437  -0.813   1.444  1.00  0.00           H  
HETATM   19  H3  UNL     1       2.099  -1.527   1.955  1.00  0.00           H  
HETATM   20  H4  UNL     1      -0.177  -1.143   1.766  1.00  0.00           H  
HETATM   21  H5  UNL     1      -0.209  -1.014  -1.255  1.00  0.00           H  
HETATM   22  H6  UNL     1      -0.415  -2.469  -0.240  1.00  0.00           H  
HETATM   23  H7  UNL     1      -2.488  -0.785  -1.281  1.00  0.00           H  
HETATM   24  H8  UNL     1      -2.466  -3.016   0.183  1.00  0.00           H  
HETATM   25  H9  UNL     1      -2.544  -0.283   1.688  1.00  0.00           H  
HETATM   26  H10 UNL     1      -4.148   0.581   0.109  1.00  0.00           H  
HETATM   27  H11 UNL     1      -2.827   1.366  -0.880  1.00  0.00           H  
HETATM   28  H12 UNL     1      -2.635   2.934   0.559  1.00  0.00           H  
HETATM   29  H13 UNL     1       0.530   2.302  -1.318  1.00  0.00           H  
CONECT    1    2    2   17
CONECT    2    3   16
CONECT    3    4    4   18
CONECT    4    5   19
CONECT    5    6   14
CONECT    6    7   13   20
CONECT    7    8   21   22
CONECT    8    9   10   23
CONECT    9   24
CONECT   10   11   13   25
CONECT   11   12   26   27
CONECT   12   28
CONECT   14   15   16   16
CONECT   15   29
END

NP0002699
     RDKit          3D

29 30  0  0  0  0  0  0  0  0999 V2000
    5.0504    0.9901   -0.3086 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.8442    0.6018   -0.0251 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6000   -0.3683    0.9254 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3152   -0.7634    1.2088 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2900   -0.2014    0.5561 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0766   -0.5831    0.8190 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.6608   -1.4125   -0.3240 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1321   -1.1035   -0.2820 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8910   -2.1267    0.2474 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1805    0.0574    0.6919 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.1504    1.0765    0.1364 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2095    2.2058    0.9494 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8994    0.5579    0.7905 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5201    0.7556   -0.3825 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4481    1.3320   -1.0538 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7802    1.1351   -0.6524 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1949    1.7129   -1.0201 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4373   -0.8132    1.4445 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0995   -1.5266    1.9545 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1775   -1.1429    1.7658 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2092   -1.0143   -1.2546 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4148   -2.4688   -0.2405 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4880   -0.7854   -1.2808 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4662   -3.0160    0.1831 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5444   -0.2830    1.6877 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1476    0.5810    0.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8265    1.3664   -0.8801 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6350    2.9343    0.5589 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298    2.3024   -1.3185 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  3
  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
  8 10  1  0
 10 11  1  0
 11 12  1  0
 10 13  1  0
  5 14  1  0
 14 15  1  0
 14 16  2  0
 16  2  1  0
 13  6  1  0
  1 17  1  0
  3 18  1  0
  4 19  1  0
  6 20  1  1
  7 21  1  0
  7 22  1  0
  8 23  1  6
  9 24  1  0
 10 25  1  1
 11 26  1  0
 11 27  1  0
 12 28  1  0
 15 29  1  0
M  END

View in JSmol

Synonyms

Value	Source
NV-02C	ChEMBL
1-(2-Deoxy-beta-L-erythropentafuranosyl)-5-methyl-2,4(1H)-pyrimidinone	MeSH

Chemical Formula

C₉H₁₃N₃O₄

Average Mass

227.2172 Da

Monoisotopic Mass

227.09061 Da

IUPAC Name

1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol

Traditional Name

1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-iminopyrimidin-2-ol

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)C[C@]([H])(O[C@@]1([H])CO)N1C=CC(=N)N=C1O

InChI Identifier

InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8+/m1/s1

InChI Key

CKTSBUTUHBMZGZ-CHKWXVPMSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, simulated)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Not Available

Species

Species of Origin

Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as pyrimidine 2'-deoxyribonucleosides. These are compounds consisting of a pyrimidine linked to a ribose which lacks a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleosides

Sub Class

Pyrimidine 2'-deoxyribonucleosides

Direct Parent

Pyrimidine 2'-deoxyribonucleosides

Alternative Parents

Substituents

Pyrimidine 2'-deoxyribonucleoside
Aminopyrimidine
Pyrimidone
Hydropyrimidine
Pyrimidine
Imidolactam
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Azacycle
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Primary amine
Primary alcohol
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Organic nitrogen compound
Amine
Aromatic heteromonocyclic compound

Molecular Framework

Aromatic heteromonocyclic compounds

External Descriptors

pyrimidine 2'-deoxyribonucleoside (CHEBI:43597 )

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	-1.5	ALOGPS
logP	-0.92	ChemAxon
logS	-2.1	ALOGPS
pKa (Strongest Acidic)	9.24	ChemAxon
pKa (Strongest Basic)	2.55	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	109.37 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	64.45 m³·mol⁻¹	ChemAxon
Polarizability	21.82 Å³	ChemAxon
Number of Rings	2	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	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

140145

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL: BioMagResBank. Nucleic Acids Res. 2008 Jan;36(Database issue):D402-8. doi: 10.1093/nar/gkm957. Epub 2007 Nov 4. [PubMed:17984079 ]

Showing NP-Card for 2'-Deoxycytidine (NP0002699)

MOL for NP0002699 (2'-Deoxycytidine)

3D MOL for NP0002699 (2'-Deoxycytidine)

3D SDF for NP0002699 (2'-Deoxycytidine)

3D-SDF for NP0002699 (2'-Deoxycytidine)

PDB for NP0002699 (2'-Deoxycytidine)

3D PDB for NP0002699 (2'-Deoxycytidine)

SMILES for NP0002699 (2'-Deoxycytidine)

INCHI for NP0002699 (2'-Deoxycytidine)

Structure for NP0002699 (2'-Deoxycytidine)

3D Structure for NP0002699 (2'-Deoxycytidine)