Structure of PDB 2pk3 Chain A Binding Site BS01

Receptor Information
>2pk3 Chain A (length=309) Species: 143495 (Aneurinibacillus thermoaerophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRALITGVAGFVGKYLANHLTEQNVEVFGTSRNNEAKLPNVEMISLDIMD
SQRVKKVISDIKPDYIFHLAAKSSVKDSWLNKKGTFSTNVFGTLHVLDAV
RDSNLDCRILTIGSSEEYGMILPEESPVSEENQLRPMSPYGVSKASVGML
ARQYVKAYGMDIIHTRTFNHIGPGQSLGFVTQDFAKQIVDIEMEKQEPII
KVGNLEAVRDFTDVRDIVQAYWLLSQYGKTGDVYNVCSGIGTRIQDVLDL
LLAMANVKIDTELNPLQLRPSEVPTLIGSNKRLKDSTGWKPRIPLEKSLF
EILQSYRQA
Ligand information
Ligand IDA2R
InChIInChI=1S/C15H24N5O17P3/c16-12-7-13(18-3-17-12)20(4-19-7)14-11(36-38(25,26)27)9(22)6(34-14)2-33-40(30,31)37-39(28,29)32-1-5-8(21)10(23)15(24)35-5/h3-6,8-11,14-15,21-24H,1-2H2,(H,28,29)(H,30,31)(H2,16,17,18)(H2,25,26,27)/t5-,6-,8-,9-,10-,11-,14-,15-/m1/s1
InChIKeyICNHOLCERMYLRZ-KEOHHSTQSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O[P](O)(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)OP(=O)(O)O)N
ACDLabs 10.04O=P(O)(O)OC3C(O)C(OC3n1c2ncnc(N)c2nc1)COP(=O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)OP(=O)(O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O[P](O)(O)=O
FormulaC15 H24 N5 O17 P3
Name[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000044460250
PDB chain2pk3 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2pk3 The structural basis for catalytic function of GMD and RMD, two closely related enzymes from the GDP-D-rhamnose biosynthesis pathway.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		G10 F11 V12 R32 D47 I48 L69 A70 A71 S73 I112 Y140 K144 H170
Binding residue
(residue number reindexed from 1)		G10 F11 V12 R32 D47 I48 L69 A70 A71 S73 I112 Y140 K144 H170
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) S114 S115 E116 Y140 K144
Catalytic site (residue number reindexed from 1) S114 S115 E116 Y140 K144
Enzyme Commision number 1.1.1.281: GDP-4-dehydro-6-deoxy-D-mannose reductase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0033705 GDP-4-dehydro-6-deoxy-D-mannose reductase activity

View graph for
Molecular Function
External links
PDB RCSB:2pk3, PDBe:2pk3, PDBj:2pk3
PDBsum2pk3
PubMed19459932
UniProtQ6T1X6|RMD_ANETH GDP-6-deoxy-D-mannose reductase (Gene Name=rmd)

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