PDB Chemical Component N5M

Ideal Model

Chemical Description

Name 5-nitrocytidine 5'-(dihydrogen phosphate)
Formula C9 H13 N4 O10 P
Formal charge 0
Molecular weight 368.194 g/mol
Component type RNA linking
Nonstandard Parent Id C

Chemical features

Atom count 37
Chiral atom count 4
Chiral atoms C1' C2' C3' C4'
Observed leaving atoms OP3 HO3'
Bond count 38
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 5-nitrocytidine 5'-(dihydrogen phosphate)
Systematic name (OpenEye OEToolkits) [(2R,3S,4R,5R)-5-(4-amino-5-nitro-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) NC1=NC(=O)N(C=C1[N+]([O-])=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
SMILES (CACTVS) NC1=NC(=O)N(C=C1[N+]([O-])=O)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
Stereo SMILES (OpenEye) C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)[N+](=O)[O-]
InChI descriptor InChI=1S/C9H13N4O10P/c10-7-3(13(17)18)1-12(9(16)11-7)8-6(15)5(14)4(23-8)2-22-24(19,20)21/h1,4-6,8,14-15H,2H2,(H2,10,11,16)(H2,19,20,21)/t4-,5-,6-,8-/m1/s1
InChIKey descriptor QPCLJXMRTPOKPG-UAKXSSHOSA-N

Status Information

Last modified 2011-06-04
Created 2007-12-28
Release status REL
Model PDB code 3BSN
Processing site RCSB