Structure of PDB 8xkf Chain E Binding Site BS01

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 IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[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[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain8xkf Chain E Residue 502 [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)		L41 A42 A43 G44 S46 R47 R48 K55 S109 R110 S113 D130 K227
Binding residue
(residue number reindexed from 1)		L12 A13 A14 G15 S17 R18 R19 K26 S80 R81 S84 D101 K198
Annotation score4
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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