Structure of PDB 2jkv Chain F Binding Site BS01

Receptor Information
>2jkv Chain F (length=471) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQADIALIGLAVMGQNLILNMNDHGFVVCAFNRTVSKVDDFLANEAKGTK
VVGAQSLKEMVSKLKKPRRIILLVKAGQAVDDFIEKLVPLLDTGDIIIDG
GNSEYRDTTRRCRDLKAKGILFVGSGVSGGEEGARYGPSLMPGGNKEAWP
HIKTIFQGIAAKVGTGEPCCDWVGDEGAGHFVKMVHNGIEYGDMQLICEA
YHLMKDVLGMAQDEMAQAFEDWNKTELDSFLIEITANILKFQDTDGKHLL
PKIRDSAGQKGTGKWTAISALEYGVPVTLIGEAVFARCLSSLKDERIQAS
KKLKGPQKFQFDGDKKSFLEDIRKALYASKIISYAQGFMLLRQAATEFGW
TLNYGGIALMWRGGCIIRSVFLGKIKDAFDRNPELQNLLLDDFFKSAVEN
CQDSWRRAVSTGVQAGIPMPCFTTALSFYDGYRHEMLPASLIQAQRDYFG
AHTYELLAKPGQFIHTNWTGH
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain2jkv Chain E Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2jkv Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A
Resolution2.532 Å
Binding residue
(original residue number in PDB)		A12 V13 M14 N33 R34 T35 K38 L74 V75 K76 A80 F84 G102 N103
Binding residue
(residue number reindexed from 1)		A11 V12 M13 N32 R33 T34 K37 L73 V74 K75 A79 F83 G101 N102
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S129 K184 H187 N188 E191
Catalytic site (residue number reindexed from 1) S128 K183 H186 N187 E190
Enzyme Commision number 1.1.1.44: phosphogluconate dehydrogenase (NADP(+)-dependent, decarboxylating).
Gene Ontology
Molecular Function
GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity
GO:0016491 oxidoreductase activity
GO:0050661 NADP binding
Biological Process
GO:0006098 pentose-phosphate shunt
GO:0009051 pentose-phosphate shunt, oxidative branch
GO:0019322 pentose biosynthetic process
GO:0019521 D-gluconate metabolic process
GO:0046177 D-gluconate catabolic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2jkv, PDBe:2jkv, PDBj:2jkv
PDBsum2jkv
PubMed
UniProtP52209|6PGD_HUMAN 6-phosphogluconate dehydrogenase, decarboxylating (Gene Name=PGD)

[Back to BioLiP]