Structure of PDB 8xkf Chain D Binding Site BS03

Receptor Information
>8xkf Chain D (length=375) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHIKQTSVVLLAAGESRRFSQTIKKQWLRSNHTPLWLSVYESFKEALDFK
EIILVVSELDYIYIKRHYPEIKLVKGGASRQESVRNALKIIDSAYTLTSD
VARGLANIEALKNLFLTLQQTSHYCIAPYLPCYDTAIYYNEALDREAIKL
IQTPQLSHTKALQSALNQGDFKDESSAILQAFPDRVSYIEGSKDLHKLTT
SGDLKHFTLFFNPAKDTFIGMGFDTHAFIKDKPMVLGGVVLDCEFGLKAH
SDGDALLHAVIDAILGAIKGGDIGEWFPDNDPKYKNASSKELLKIVLDFS
QSIGFELFEMGATIFSEIPKITPYKPAILENLSQLLGLEKSQISLKATTM
EKMGFIGKQEGLLVQAHVSMRYKQK
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain8xkf Chain D Residue 505 [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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PDB8xkf Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D254 H256 H288
Binding residue
(residue number reindexed from 1)		D224 H226 H258
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.60: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase.
4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016779 nucleotidyltransferase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0050518 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
GO:0070567 cytidylyltransferase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8xkf, PDBe:8xkf, PDBj:8xkf
PDBsum8xkf
PubMed38537721
UniProtO25664|ISPDF_HELPY Bifunctional enzyme IspD/IspF (Gene Name=ispDF)

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