PDB Chemical Component 5PY

Ideal Model

Chemical Description

Name 1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE
Formula C10 H15 N2 O7 P
Formal charge 0
Molecular weight 306.209 g/mol
Component type DNA LINKING
Nonstandard Parent Id DT

Chemical features

Atom count 35
Chiral atom count 3
Chiral atoms C4' C1' C3'
Observed leaving atoms OP3 HO3'
Bond count 36
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methylpyrimidin-2(1H)-one
Systematic name (OpenEye OEToolkits) [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1
SMILES (CACTVS) CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1
Stereo SMILES (OpenEye) CC1=CN(C(=O)N=C1)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
InChI descriptor InChI=1S/C10H15N2O7P/c1-6-3-11-10(14)12(4-6)9-2-7(13)8(19-9)5-18-20(15,16)17/h3-4,7-9,13H,2,5H2,1H3,(H2,15,16,17)/t7-,8+,9+/m0/s1
InChIKey descriptor TWYWJJKQSULVQX-DJLDLDEBSA-N

Status Information

Last modified 2011-06-04
Created 2006-10-12
Release status REL
Processing site RCSB