PDB Chemical Component 5HM

Ideal Model

Chemical Description

Name 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
Synonyms 5-hydroxymethylcytidine 5'-monophosphate
Formula C10 H16 N3 O9 P
Formal charge 0
Molecular weight 353.223 g/mol
Component type RNA LINKING
Nonstandard Parent Id C

Chemical features

Atom count 39
Chiral atom count 4
Chiral atoms C4' C3' C2' C1'
Observed leaving atoms OP3 HO3'
Bond count 40
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
Systematic name (OpenEye OEToolkits) [(2R,3S,4R,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) NC1=NC(=O)N(C=C1CO)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
SMILES (CACTVS) NC1=NC(=O)N(C=C1CO)[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)CO
InChI descriptor InChI=1S/C10H16N3O9P/c11-8-4(2-14)1-13(10(17)12-8)9-7(16)6(15)5(22-9)3-21-23(18,19)20/h1,5-7,9,14-16H,2-3H2,(H2,11,12,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1
InChIKey descriptor KPUOHXMVCZBWQC-JXOAFFINSA-N

Status Information

Last modified 2020-06-17
Created 2014-01-22
Release status REL
Model PDB code 4OHB
Processing site PDBJ