Structure of PDB 1i8j Chain A Binding Site BS02

Receptor Information
>1i8j Chain A (length=323) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMP
GVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVAR
MSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQA
VVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFY
GPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGA
YLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSI
KRAGADLIFSYFALDLAEKKILR
Ligand information
Ligand IDDSB
InChIInChI=1S/C10H14O6/c11-7(3-5-9(13)14)1-2-8(12)4-6-10(15)16/h1-6H2,(H,13,14)(H,15,16)
InChIKeyDUAWJQCMZICMIK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(CCC(=O)CCC(=O)O)CCC(=O)O
CACTVS 3.341OC(=O)CCC(=O)CCC(=O)CCC(O)=O
OpenEye OEToolkits 1.5.0C(CC(=O)CCC(=O)O)C(=O)CCC(=O)O
FormulaC10 H14 O6
Name4,7-DIOXOSEBACIC ACID
ChEMBL
DrugBankDB04560
ZINCZINC000003870974
PDB chain1i8j Chain A Residue 350 [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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PDB1i8j Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		K194 Y200 F203 R204 R215 Q219 K246 Y269 V271 S272 Y311
Binding residue
(residue number reindexed from 1)		K194 Y200 F203 R204 R215 Q219 K246 Y269 V271 S272 Y311
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=4.41,IC50=39uM
Enzymatic activity
Catalytic site (original residue number in PDB) K194 K246
Catalytic site (residue number reindexed from 1) K194 K246
Enzyme Commision number 4.2.1.24: porphobilinogen synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004655 porphobilinogen synthase activity
GO:0008270 zinc ion binding
GO:0016829 lyase activity
GO:0046872 metal ion binding
Biological Process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0006783 heme biosynthetic process
GO:0033014 tetrapyrrole biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1i8j, PDBe:1i8j, PDBj:1i8j
PDBsum1i8j
PubMed11444968
UniProtP0ACB2|HEM2_ECOLI Delta-aminolevulinic acid dehydratase (Gene Name=hemB)

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