Structure of PDB 2iz0 Chain C Binding Site BS01

Receptor Information
>2iz0 Chain C (length=468) Species: 1358 (Lactococcus lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AQANFGVVGMAVMGKNLALNVESRGYTVAIYNRTTSKTEEVFKEHQDKNL
VFTKTLEEFVGSLEKPRRIMLMVQAGAATDATIKSLLPLLDIGDILIDGG
NTHFPDTMRRNAELADSGINFIGTGVSGGEKGALLGPSMMPGGQKEAYDL
VAPIFEQIAAKAPQDGKPCVAYMGANGAGHYVKMVHNGIEYGDMQLIAES
YDLLKRILGLSNAEIQAIFEEWNEGELDSYLIEITKEVLKRKDDEGEGYI
VDKILDKAGNKGTGKWTSESALDLGVPLPLITESVFARYISTYKDERVKA
SKVLSGPALDFSGDKKEVIEKIRKALYFSKIMSYAQGFAQLRKASEEFDW
DLPYGTIAQIWRAGCIIRAEFLQNITDAFDKDSELENLLLDDYFVDITKR
YQEAVRDVVSLAVQAGTPIPTFTSAISYYDSYRSENLPANLIQAQRDYFG
AHTYERTDKAGIFHYDWY
Ligand information
Ligand IDATR
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(27-29(17,18)19)6(16)4(26-10)1-25-31(23,24)28-30(20,21)22/h2-4,6-7,10,16H,1H2,(H,23,24)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKeyYPTPYQSAVGGMFN-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O[P](O)(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)OP(=O)(O)O)O)OP(=O)(O)O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(OP(=O)(O)O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O[P](O)(O)=O
FormulaC10 H16 N5 O13 P3
Name2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB02363
ZINCZINC000013523101
PDB chain2iz0 Chain C Residue 1470 [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]
PDB2iz0 Crystal Structures of a Bacterial 6- Phosphogluconate Dehydrogenase Reveal Aspects of Specificity, Mechanism and Mode of Inhibition by Analogues of High-Energy Reaction Intermediates.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		N33 R34 T35 K38 V74 Q75 A79
Binding residue
(residue number reindexed from 1)		N32 R33 T34 K37 V73 Q74 A78
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) S128 K184 H187 N188 E191
Catalytic site (residue number reindexed from 1) S127 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:0016054 organic acid catabolic process
GO:0019521 D-gluconate metabolic process
GO:0046177 D-gluconate catabolic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2iz0, PDBe:2iz0, PDBj:2iz0
PDBsum2iz0
PubMed17222187
UniProtP96789|6PGD_LACLM 6-phosphogluconate dehydrogenase, decarboxylating (Gene Name=gnd)

[Back to BioLiP]