Structure of PDB 3b7j Chain A Binding Site BS01

Receptor Information

>3b7j Chain A (length=152) Species: 210 (Helicobacter pylori)

LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNG
HFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKV
KFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAE
RE

Ligand information

• Ligand ID: JUG
• InChI: InChI=1S/C10H6O3/c11-7-4-5-9(13)10-6(7)2-1-3-8(10)12/h1-5,12H
• InChIKey: KQPYUDDGWXQXHS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Oc1cccc2C(=O)C=CC(=O)c12
  ACDLabs 10.04: O=C2c1c(c(O)ccc1)C(=O)C=C2
  OpenEye OEToolkits 1.5.0: c1cc2c(c(c1)O)C(=O)C=CC2=O
• Formula: C10 H6 O3
• Name: 5-hydroxynaphthalene-1,4-dione;
  Juglone
• ChEMBL: CHEMBL43612
• ZINC: ZINC000000526257
• PDB chain: 3b7j Chain B Residue 163

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3b7j Natural product juglone targets three key enzymes from Helicobacter pylori: inhibition assay with crystal structure characterization
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): I64 F109 R110 I111 P112
• Binding residue (residue number reindexed from 1): I57 F102 R103 I104 P105
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.17,Ki=6.8uM

Enzymatic activity

• Catalytic site (original residue number in PDB): H58 I64 G67 V68 E72
• Catalytic site (residue number reindexed from 1): H51 I57 G60 V61 E65
• 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

External links

• PDB: RCSB:3b7j, PDBe:3b7j, PDBj:3b7j
• PDBsum: 3b7j
• PubMed: 18565285
• UniProt: Q5G940