PDB Chemical Component URX

Ideal Model

Chemical Description

Name [(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate
Formula C12 H17 N2 O8 P
Formal charge 0
Molecular weight 348.246 g/mol
Component type DNA linking
Nonstandard Parent Id DU

Chemical features

Atom count 40
Chiral atom count 5
Chiral atoms C1' C2' C3' C4' C6'
Observed leaving atoms OP3 HO3' HOP3
Bond count 42
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) [(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl dihydrogen phosphate
Systematic name (OpenEye OEToolkits) [(1R,2R,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methyl-5-oxabicyclo[2.2.1]heptan-4-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) C[C@@H]1C[C@]2(CO[P](O)(O)=O)O[C@H]([C@H]1[C@@H]2O)N3C=CC(=O)NC3=O
SMILES (CACTVS) C[CH]1C[C]2(CO[P](O)(O)=O)O[CH]([CH]1[CH]2O)N3C=CC(=O)NC3=O
Stereo SMILES (OpenEye) C[C@@H]1C[C@]2([C@H]([C@@H]1[C@@H](O2)N3C=CC(=O)NC3=O)O)COP(=O)(O)O
InChI descriptor InChI=1S/C12H17N2O8P/c1-6-4-12(5-21-23(18,19)20)9(16)8(6)10(22-12)14-3-2-7(15)13-11(14)17/h2-3,6,8-10,16H,4-5H2,1H3,(H,13,15,17)(H2,18,19,20)/t6-,8-,9+,10-,12-/m1/s1
InChIKey descriptor BIKPERMTZJFCSY-VOLLVAIWSA-N

Status Information

Last modified 2011-06-04
Created 2010-10-11
Release status REL
Model PDB code 3OZ4
Processing site RCSB