Np mrd loader

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

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Record Information
Version2.0
Created at2020-11-23 19:38:15 UTC
Updated at2021-08-12 19:51:53 UTC
NP-MRD IDNP0002699
Secondary Accession NumbersNone
Natural Product Identification
Common Name2'-Deoxycytidine
Provided ByBMRBBMRB logo
Description 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
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0002699 (2'-Deoxycytidine)


     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
Download

3D MOL for NP0002699 (2'-Deoxycytidine)

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
Download

3D SDF for NP0002699 (2'-Deoxycytidine)


     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

$$$$
Download

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

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
Download

PDB for NP0002699 (2'-Deoxycytidine)

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
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3D PDB for NP0002699 (2'-Deoxycytidine)

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
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SMILES for NP0002699 (2'-Deoxycytidine)

[H][C@@]1(O)C[C@]([H])(O[C@@]1([H])CO)N1C=CC(=N)N=C1O
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INCHI for NP0002699 (2'-Deoxycytidine)

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
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Synonyms
ValueSource
NV-02CChEMBL
1-(2-Deoxy-beta-L-erythropentafuranosyl)-5-methyl-2,4(1H)-pyrimidinoneMeSH
Chemical FormulaC9H13N3O4
Average Mass227.2172 Da
Monoisotopic Mass227.09061 Da
IUPAC Name1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-imino-1,4-dihydropyrimidin-2-ol
Traditional Name1-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-iminopyrimidin-2-ol
CAS Registry NumberNot 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 KeyCKTSBUTUHBMZGZ-CHKWXVPMSA-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
DescriptionThis 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.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassPyrimidine 2'-deoxyribonucleosides
Direct ParentPyrimidine 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 FrameworkAromatic 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-1.5ALOGPS
logP-0.92ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)9.24ChemAxon
pKa (Strongest Basic)2.55ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area109.37 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity64.45 m³·mol⁻¹ChemAxon
Polarizability21.82 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 ID140145
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Good Scents IDNot Available
References
General References