Structure of PDB 8xkf Chain D Binding Site BS02

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 IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain8xkf Chain D Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		S346 K350 I351 T352 A377 T378 T379
Binding residue
(residue number reindexed from 1)		S316 K320 I321 T322 A347 T348 T349
Annotation score3
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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