PDB Chemical Component 6OP

Ideal Model

Chemical Description

Name 1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione
Formula C14 H21 N2 O9 P
Formal charge 0
Molecular weight 392.298 g/mol
Component type RNA linking

Chemical features

Atom count 47
Chiral atom count 4
Chiral atoms C4' C3' C2' C1'
Observed leaving atoms OP3 HOP3 HO3'
Bond count 48
Aromatic bond count 0

Chemical Identifiers

Systematic name (ACDLabs) 1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione
Systematic name (OpenEye OEToolkits) [(~{E})-2-[(2~{R},3~{R},4~{R},5~{R})-4-(2-methoxyethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]ethenyl]phosphonic acid

Chemical Descriptors

Stereo SMILES (CACTVS) COCCO[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=C(C)C(=O)NC2=O)/C=C/[P](O)(O)=O
SMILES (CACTVS) COCCO[CH]1[CH](O)[CH](O[CH]1N2C=C(C)C(=O)NC2=O)C=C[P](O)(O)=O
Stereo SMILES (OpenEye) CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)/C=C/P(=O)(O)O)O)OCCOC
InChI descriptor InChI=1S/C14H21N2O9P/c1-8-7-16(14(19)15-12(8)18)13-11(24-5-4-23-2)10(17)9(25-13)3-6-26(20,21)22/h3,6-7,9-11,13,17H,4-5H2,1-2H3,(H,15,18,19)(H2,20,21,22)/b6-3+/t9-,10-,11-,13-/m1/s1
InChIKey descriptor MIWMWNWNEZHLGC-PSDJLLRUSA-N

Status Information

Last modified 2016-07-15
Created 2016-05-13
Release status REL
Model PDB code 5JS2
Processing site RCSB