PDB Chemical Component 4U3

Ideal Model

Chemical Description

Name 5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)
Synonyms 5-Chloro-5'-deoxycytidine
Formula C9 H13 Cl N3 O7 P
Formal charge 0
Molecular weight 341.642 g/mol
Component type DNA linking
Nonstandard Parent Id DC

Chemical features

Atom count 34
Chiral atom count 3
Chiral atoms C4' C3' C1'
Observed leaving atoms OP3 HOP3
Bond count 35
Aromatic bond count 0

Chemical Identifiers

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

Chemical Descriptors

Stereo SMILES (CACTVS) NC1=NC(=O)N(C=C1Cl)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
SMILES (CACTVS) NC1=NC(=O)N(C=C1Cl)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
Stereo SMILES (OpenEye) C1[C@@H]([C@H](O[C@H]1N2C=C(C(=NC2=O)N)Cl)COP(=O)(O)O)O
InChI descriptor InChI=1S/C9H13ClN3O7P/c10-4-2-13(9(15)12-8(4)11)7-1-5(14)6(20-7)3-19-21(16,17)18/h2,5-7,14H,1,3H2,(H2,11,12,15)(H2,16,17,18)/t5-,6+,7+/m0/s1
InChIKey descriptor JXVVNBLPBHXIAA-RRKCRQDMSA-N

Status Information

Last modified 2020-06-17
Created 2015-05-27
Release status REL
Model PDB code 5BOM
Processing site RCSB