Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

CDM : Summary

Code

CDM

One-letter code

X

Molecule name

4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-O-[(R)-hydroxy{[(S)-hydroxy{[(2R,3S)-2,3,4-trihydroxy-3-methylbutyl]oxy}phosphoryl]oxy}phosphoryl]cytidine
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(2R,3S)-2,3,4-trihydroxy-3-methyl-butoxy]phosphoryl] hydrogen phosphate

Formula

C14 H25 N3 O14 P2

Formal charge

0

Molecular weight

521.308 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(OCC(O)C(O)(C)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
SMILES CACTVS 3.341 C[C](O)(CO)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N
SMILES OpenEye OEToolkits 1.5.0 CC(CO)(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)O)O
Canonical SMILES CACTVS 3.341 C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O)O

IUPAC InChI

InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1

IUPAC InChI key

YFAUKWZNPVBCFF-XHIBXCGHSA-N
CDM

wwPDB Information

Atom count

58 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-05-22

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned