PDB Chemical Component US3

Ideal Model

Chemical Description

Name 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one
Synonyms 2-Se-Thymidine-5'-phosphate
Formula C10 H15 N2 O7 P Se
Formal charge 0
Molecular weight 385.169 g/mol
Component type DNA LINKING
Nonstandard Parent Id DT

Chemical features

Atom count 36
Chiral atom count 3
Chiral atoms C1' C3' C4'
Observed leaving atoms OP3 HOP3
Bond count 37
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one
Systematic name (OpenEye OEToolkits) [(2R,3S,5R)-3-hydroxy-5-(5-methyl-4-oxo-2-selanyl-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(=NC1=O)[SeH]
SMILES (CACTVS) CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=NC1=O)[SeH]
Stereo SMILES (OpenEye) CC1=CN(C(=NC1=O)[SeH])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O
InChI descriptor InChI=1S/C10H15N2O7PSe/c1-5-3-12(10(21)11-9(5)14)8-2-6(13)7(19-8)4-18-20(15,16)17/h3,6-8,13H,2,4H2,1H3,(H,11,14,21)(H2,15,16,17)/t6-,7+,8+/m0/s1
InChIKey descriptor NJOAZAGHIQNDNL-XLPZGREQSA-N

Status Information

Last modified 2021-03-01
Created 2009-06-15
Release status REL
Model PDB code 3HGD
Processing site RCSB