PDB Chemical Component RY

Ideal Model

Chemical Description

Name 5'-3,6-dihydrocytidylic acid
Formula C9 H16 N3 O8 P
Formal charge 0
Molecular weight 325.212 g/mol
Component type RNA linking

Chemical features

Atom count 37
Chiral atom count 4
Chiral atoms C4' C3' C2' C1'
Observed leaving atoms OP3
Bond count 38
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 5'-3,6-dihydrocytidylic acid
Systematic name (OpenEye OEToolkits) [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Chemical Descriptors

Stereo SMILES (CACTVS) NC1=CCN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N1
SMILES (CACTVS) NC1=CCN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N1
Stereo SMILES (OpenEye) C1C=C(NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N
InChI descriptor InChI=1S/C9H16N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1,4,6-8,13-14H,2-3,10H2,(H,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKey descriptor NWPXZYGTNOANAA-XVFCMESISA-N

Status Information

Last modified 2018-10-26
Created 2018-09-06
Release status REL
Model PDB code 6MCF
Processing site RCSB