PDB Chemical Component US5

Ideal Model

Chemical Description

Name 1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one
Synonyms 4-Se-ribouridine-5'-phosphate
Formula C9 H13 N2 O8 P Se
Formal charge 0
Molecular weight 387.142 g/mol
Component type RNA LINKING
Nonstandard Parent Id U

Chemical features

Atom count 34
Chiral atom count 4
Chiral atoms C1' C2' C3' C4'
Observed leaving atoms OP3 HOP3
Bond count 35
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one
Systematic name (OpenEye OEToolkits) [(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxo-4-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)[SeH]
SMILES (CACTVS) O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)[SeH]
Stereo SMILES (OpenEye) C1=CN(C(=O)N=C1[SeH])[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
InChI descriptor InChI=1S/C9H13N2O8PSe/c12-6-4(3-18-20(15,16)17)19-8(7(6)13)11-2-1-5(21)10-9(11)14/h1-2,4,6-8,12-13H,3H2,(H,10,14,21)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1
InChIKey descriptor ZCQCFKOZDRTETH-XVFCMESISA-N

Status Information

Last modified 2021-03-01
Created 2009-07-17
Release status REL
Model PDB code 3HGA
Processing site RCSB