PDB Chemical Component D3N

Ideal Model

Chemical Description

Name 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one
Formula C16 H17 N2 O7 P
Formal charge 0
Molecular weight 380.289 g/mol
Component type DNA LINKING

Chemical features

Atom count 43
Chiral atom count 3
Chiral atoms C4' C3' C1'
Observed leaving atoms OP3 H2
Bond count 46
Aromatic bond count 11

Chemical Identifiers

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

Chemical Descriptors

Stereo SMILES (CACTVS) O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C(=O)Nc3cccc4cccc2c34
SMILES (CACTVS) O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C(=O)Nc3cccc4cccc2c34
Stereo SMILES (OpenEye) c1cc2cccc3c2c(c1)NC(=O)N3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O
InChI descriptor InChI=1S/C16H17N2O7P/c19-12-7-14(25-13(12)8-24-26(21,22)23)18-11-6-2-4-9-3-1-5-10(15(9)11)17-16(18)20/h1-6,12-14,19H,7-8H2,(H,17,20)(H2,21,22,23)/t12-,13+,14+/m0/s1
InChIKey descriptor SQPAXPCPGSJUFJ-BFHYXJOUSA-N

Status Information

Last modified 2013-06-07
Created 2012-11-02
Release status REL
Model PDB code 4HQI
Processing site RCSB