PDB Chemical Component DDN

Ideal Model

Chemical Description

Name 3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Synonyms ((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE
Formula C9 H15 N2 O8 P
Formal charge 0
Molecular weight 310.198 g/mol
Component type DNA LINKING
Nonstandard Parent Id DU

Chemical features

Atom count 35
Chiral atom count 4
Chiral atoms C4' C3' C1' C4
Observed leaving atoms OP3
Bond count 36
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) (4R)-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
Systematic name (OpenEye OEToolkits) [(2R,3S,5R)-3-hydroxy-5-[(4R)-4-hydroxy-2-oxo-3,4-dihydropyrimidin-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=C[C@@H](O)NC2=O
SMILES (CACTVS) O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C[CH](O)NC2=O
Stereo SMILES (OpenEye) C1[C@@H]([C@H](O[C@H]1N2C=C[C@H](NC2=O)O)COP(=O)(O)O)O
InChI descriptor InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-8,12-13H,3-4H2,(H,10,14)(H2,15,16,17)/t5-,6+,7+,8+/m0/s1
InChIKey descriptor ILSIYJVILUIVPM-LXGUWJNJSA-N

Status Information

Last modified 2021-03-13
Created 2004-12-14
Release status REL
Model PDB code 1VQ2
Processing site RCSB