PDB Chemical Component XCY

Ideal Model

Chemical Description

Name {5-[4-{[4-(AMINOMETHYL)BENZYL]AMINO}-2-OXOPYRIMIDIN-1(2H)- YL]-3-HYDROXYTETRAHYDROFURAN-2-YL}METHYL DIHYDROGEN PHOSPHATE
Formula C17 H23 N4 O7 P
Formal charge 0
Molecular weight 426.361 g/mol
Component type DNA LINKING
Nonstandard Parent Id DC

Chemical features

Atom count 52
Chiral atom count 3
Chiral atoms C4' C1' C3'
Observed leaving atoms OP3 HO3'
Bond count 54
Aromatic bond count 6

Chemical Identifiers

Systematic name (ACDLabs) N-[4-(aminomethyl)benzyl]-2'-deoxycytidine 5'-(dihydrogen phosphate)
Systematic name (OpenEye OEToolkits) [(2R,3S,5R)-5-[4-[[4-(aminomethyl)phenyl]methylamino]-2-oxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) NCc1ccc(CNC2=NC(=O)N(C=C2)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)cc1
SMILES (CACTVS) NCc1ccc(CNC2=NC(=O)N(C=C2)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)cc1
Stereo SMILES (OpenEye) c1cc(ccc1CN)CNC2=NC(=O)N(C=C2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O
InChI descriptor InChI=1S/C17H23N4O7P/c18-8-11-1-3-12(4-2-11)9-19-15-5-6-21(17(23)20-15)16-7-13(22)14(28-16)10-27-29(24,25)26/h1-6,13-14,16,22H,7-10,18H2,(H,19,20,23)(H2,24,25,26)/t13-,14+,16+/m0/s1
InChIKey descriptor ATPQGDDDWMERDD-SQWLQELKSA-N

Status Information

Last modified 2011-06-04
Created 2005-01-04
Release status REL
Model PDB code 1YFH
Processing site RCSB