Structure of PDB 3dp2 Chain B Binding Site BS01

Receptor Information
>3dp2 Chain B (length=150) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHF
PNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKF
RIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE
Ligand information
Ligand ID4BE
InChIInChI=1S/C14H9Br3N2O3/c15-9-3-1-7(2-4-9)14(22)19-18-6-8-5-10(16)13(21)11(17)12(8)20/h1-6,20-21H,(H,19,22)/b18-6+
InChIKeyHKNUDJDAVYPTGD-NGYBGAFCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Oc1c(Br)cc(C=NNC(=O)c2ccc(Br)cc2)c(O)c1Br
ACDLabs 10.04Brc1cc(c(O)c(Br)c1O)\C=N\NC(=O)c2ccc(Br)cc2
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)NN=Cc2cc(c(c(c2O)Br)O)Br)Br
OpenEye OEToolkits 1.5.0c1cc(ccc1C(=O)N/N=C/c2cc(c(c(c2O)Br)O)Br)Br
CACTVS 3.341Oc1c(Br)cc(/C=N/NC(=O)c2ccc(Br)cc2)c(O)c1Br
FormulaC14 H9 Br3 N2 O3
Name4-bromo-N'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]benzohydrazide
ChEMBLCHEMBL474857
DrugBankDB07098
ZINCZINC000040900664
PDB chain3dp2 Chain B Residue 162 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dp2 Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		I98 Y100 R158 E159
Binding residue
(residue number reindexed from 1)		I89 Y91 R149 E150
Annotation score1
Binding affinityMOAD: ic50=1.5uM
PDBbind-CN: -logKd/Ki=5.82,IC50=1.50uM
Enzymatic activity
Catalytic site (original residue number in PDB) H58 I64 G67 V68 E72
Catalytic site (residue number reindexed from 1) H49 I55 G58 V59 E63
Enzyme Commision number 4.2.1.59: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
GO:0019171 (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity
Biological Process
GO:0006633 fatty acid biosynthetic process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dp2, PDBe:3dp2, PDBj:3dp2
PDBsum3dp2
PubMed19309082
UniProtQ5G940

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