Structure of PDB 8xkf Chain E Binding Site BS02

Receptor Information
>8xkf Chain E (length=377) Species: 85962 (Helicobacter pylori 26695) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HHHIKQTSVVLLAAGESRRFSQTIKKQWLRSNHTPLWLSVYESFKEALDF
KEIILVVSELDYIYIKRHYPEIKLVKGGASRQESVRNALKIIDSAYTLTS
DVARGLANIEALKNLFLTLQQTSHYCIAPYLPCYDTAIYYNEALDREAIK
LIQTPQLSHTKALQSALNQGDFKDESSAILQAFPDRVSYIEGSKDLHKLT
TSGDLKHFTLFFNPAKDTFIGMGFDTHAFIKDKPMVLGGVVLDCEFGLKA
HSDGDALLHAVIDAILGAIKGGDIGEWFPDNDPKYKNASSKELLKIVLDF
SQSIGFELFEMGATIFSEIPKITPYKPAILENLSQLLGLEKSQISLKATT
MEKMGFIGKQEGLLVQAHVSMRYKQKL
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain8xkf Chain E Residue 503 [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)		S346 K350 I351 T352 A377 T378 T379 E381
Binding residue
(residue number reindexed from 1)		S317 K321 I322 T323 A348 T349 T350 E352
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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