Structure of PDB 8d4i Chain C Binding Site BS02

Receptor Information
>8d4i Chain C (length=462) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTDSIMQNYNQLREQVINGDRRFQHKDGHLCFEGVDLDALARQYPTPFYV
FSEPEIIRNIHEIQQAFAAHKNTKTFFASKTCSVMGVLKAIRDAGICAEA
NSQYEVRKCLEIGFRGDQIVFNGVVKKPADLEYAIANDLYLINVDSLYEL
EHIDAISRKLKKVANVCVRVEPNVPSLVTAFHAKSGLDLEQAEETCRRIL
AMPYVHLRGLHMHVGDQVPESEPFAKATKVLVDESRRLEEVLGIKFDLIN
VGGGIPVPYKYDDENGDPLKDNMYAGITAQDFADAVIREVHKWRTDVEIC
IEPGRKVTGSAAVLLTEVSCEKRKTNYDLNGNVECHVEWKFVDAGYSVLS
DSQHFDWFFYVYNASRMTAAHDAWIKLAGPLCDGGDYFHMGVKGEEFLLP
KETHVGDIVAFLDAGAYTIESQTVFNNRPRTGVVMIDKNGDTRLIRREDS
YEDMVKYDIYLA
Ligand information
Ligand IDEPE
InChIInChI=1S/C8H18N2O4S/c11-7-5-9-1-3-10(4-2-9)6-8-15(12,13)14/h11H,1-8H2,(H,12,13,14)
InChIKeyJKMHFZQWWAIEOD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=S(=O)(O)CCN1CCN(CCO)CC1
OpenEye OEToolkits 1.5.0C1CN(CCN1CCO)CCS(=O)(=O)O
CACTVS 3.341OCCN1CCN(CC1)CC[S](O)(=O)=O
FormulaC8 H18 N2 O4 S
Name4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID;
HEPES
ChEMBLCHEMBL1232545
DrugBankDB16872
ZINCZINC000019203136
PDB chain8d4i Chain C Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8d4i The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.
Resolution1.32 Å
Binding residue
(original residue number in PDB)		H218 G220 D221 D356 Y422
Binding residue
(residue number reindexed from 1)		H213 G215 D216 D351 Y417
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.1.116: D-ornithine/D-lysine decarboxylase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008836 diaminopimelate decarboxylase activity
GO:0016830 carbon-carbon lyase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0009089 lysine biosynthetic process via diaminopimelate

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8d4i, PDBe:8d4i, PDBj:8d4i
PDBsum8d4i
PubMed36265649
UniProtQ8ZNC4|DOKDC_SALTY D-ornithine/D-lysine decarboxylase (Gene Name=dokD)

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