Chemical Components in the PDB

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GDR : Summary

Code

GDR

One-letter code

G

Molecule name

GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE

Systematic names

ProgramVersionName
ACDLabs 10.04 [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.5.0 [[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2R,3S,4S,5S,6R)-3,4,5-trihydroxy-6-methyl-oxan-2-yl] hydrogen phosphate

Formula

C16 H25 N5 O15 P2

Formal charge

0

Molecular weight

589.342 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC4OC(n2c3N=C(N)NC(=O)c3nc2)C(O)C4O
SMILES CACTVS 3.341 C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O
Canonical SMILES CACTVS 3.341 C[C@H]1O[C@H](O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O

IUPAC InChI

InChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5-,7-,8-,9+,10-,11+,14-,15-/m1/s1

IUPAC InChI key

LQEBEXMHBLQMDB-GDJBGNAASA-N
GDR

wwPDB Information

Atom count

63 (38 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DG

Defined at

2002-11-21

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned