Structure of PDB 3dp1 Chain D Binding Site BS01

Receptor Information
>3dp1 Chain D (length=149) Species: 210 (Helicobacter pylori) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHF
PNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKF
RIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER
Ligand information
Ligand ID2RB
InChIInChI=1S/C15H12Br2N2O4/c1-23-10-4-2-8(3-5-10)15(22)19-18-7-9-6-11(16)14(21)12(17)13(9)20/h2-7,20-21H,1H3,(H,19,22)/b18-7+
InChIKeyBMGXNERTVNWBJG-CNHKJKLMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0COc1ccc(cc1)C(=O)N/N=C/c2cc(c(c(c2O)Br)O)Br
ACDLabs 10.04Brc1cc(c(O)c(Br)c1O)\C=N\NC(=O)c2ccc(OC)cc2
OpenEye OEToolkits 1.5.0COc1ccc(cc1)C(=O)NN=Cc2cc(c(c(c2O)Br)O)Br
CACTVS 3.341COc1ccc(cc1)C(=O)NN=Cc2cc(Br)c(O)c(Br)c2O
CACTVS 3.341COc1ccc(cc1)C(=O)N\N=C\c2cc(Br)c(O)c(Br)c2O
FormulaC15 H12 Br2 N2 O4
NameN'-[(1E)-(3,5-dibromo-2,4-dihydroxyphenyl)methylidene]-4-methoxybenzohydrazide
ChEMBLCHEMBL492514
DrugBankDB06978
ZINCZINC000009190152
PDB chain3dp1 Chain C Residue 161 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3dp1 Discovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F59 I64
Binding residue
(residue number reindexed from 1)		F50 I55
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.00,IC50=9.92uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dp1, PDBe:3dp1, PDBj:3dp1
PDBsum3dp1
PubMed19309082
UniProtQ5G940

[Back to BioLiP]