Structure of PDB 8d5r Chain A Binding Site BS01

Receptor Information
>8d5r Chain A (length=461) 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
EHIDAISRKLKKVANVCVRVEPNVVTAFHAKSGLDLEQAEETCRRILAMP
YVHLRGLHMHVGDQVPESEPFAKATKVLVDESRRLEEVLGIKFDLINVGG
GIPVPYKYDDENGDPLKDNMYAGITAQDFADAVIREVHKWRTDVEICIEP
GRKVTGSAAVLLTEVSCEKRKTNYDLNGNVECHVEWKFVDAGYSVLSDSQ
HFDWFFYVYNASRMTAAHDAWIKLAGPLCDGGDYFHMGVKGEEFLLPKET
HVGDIVAFLDAGAYTIESQTVFNNRPRTGVVMIDKNGDTRLIRREDSYED
MVKYDIYLAAA
Ligand information
Ligand IDORX
InChIInChI=1S/C13H22N3O7P/c1-8-12(17)10(6-16-11(13(18)19)3-2-4-14)9(5-15-8)7-23-24(20,21)22/h5,11,16-17H,2-4,6-7,14H2,1H3,(H,18,19)(H2,20,21,22)/t11-/m1/s1
InChIKeyOIRLUPUXIUAWOH-LLVKDONJSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCCN
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[C@H](CCCN)C(O)=O)c1O
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCCN)C(O)=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCCN)C(=O)O)O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCCN)C(=O)O)O
FormulaC13 H22 N3 O7 P
NameN~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-ORNITHINE
ChEMBL
DrugBank
ZINCZINC000002047626
PDB chain8d5r Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8d5r The Y430F mutant of Salmonella d-ornithine/d-lysine decarboxylase has altered stereospecificity and a putrescine allosteric activation site.
Resolution1.44 Å
Binding residue
(original residue number in PDB)		A78 K80 H218 D221 G259 E307 G309 R310 Y422
Binding residue
(residue number reindexed from 1)		A78 K80 H210 D213 G251 E299 G301 R302 Y414
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

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Molecular Function
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Biological Process
External links
PDB RCSB:8d5r, PDBe:8d5r, PDBj:8d5r
PDBsum8d5r
PubMed36265649
UniProtQ8ZNC4|DOKDC_SALTY D-ornithine/D-lysine decarboxylase (Gene Name=dokD)

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