Structure of PDB 5wdl Chain A Binding Site BS01

Receptor Information
>5wdl Chain A (length=372) Species: 435591 (Parabacteroides distasonis ATCC 8503) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GFVFTTVKENPITSVKNQNRAGTCWCYSSYSFLESELLRMGKGEYDLSEM
FTVYNTYLDRADAAVRTHGDVSFSQGGSFYDALYGMETFGLVPEEEMRPG
MMYADTLSNHTELSALTDAMVAAIAKGKLRKLQSDENNAMLWKKAVAAVH
QIYLGVPPEKFTYKGKEYTPKSFFESTGLKASDYVSLTSYTHHPFYTQFP
LEIQDNWRHGMSYNLPLDEFMEVFDNAINTGYTIAWGSDVSESGFTRDGV
AVMPDDEKVQELSSDMAHWLKLKPEEKKLNTKPQPQKWCTQAERQLAYDN
YETTDDHGMQIYGIAKDQEGNEYYMVKNSWGTNSKYNGIWYASKAFVRYK
TMNIVVHKDALPKAIKAKLGIK
Ligand information
Ligand IDR33
InChIInChI=1S/C9H19N5O2/c1-6(15)7(14-8(16)5-10)3-2-4-13-9(11)12/h7H,2-5,10H2,1H3,(H,14,16)(H4,11,12,13)/t7-/m0/s1
InChIKeyCAKKYWQZWULXCC-ZETCQYMHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6[H]/N=C(\N)/NCCC[C@@H](C(=O)C)NC(=O)CN
CACTVS 3.385CC(=O)[CH](CCCNC(N)=N)NC(=O)CN
CACTVS 3.385CC(=O)[C@H](CCCNC(N)=N)NC(=O)CN
OpenEye OEToolkits 2.0.6CC(=O)C(CCCNC(=N)N)NC(=O)CN
ACDLabs 12.01C(=O)(C)C(CCCN/C(N)=N)NC(=O)CN
FormulaC9 H19 N5 O2
NameN-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]glycinamide
ChEMBL
DrugBank
ZINC
PDB chain5wdl Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5wdl A Commensal Dipeptidyl Aminopeptidase with Specificity for N-Terminal Glycine Degrades Human-Produced Antimicrobial Peptides in Vitro.
Resolution2.625 Å
Binding residue
(original residue number in PDB)		G54 C56 G108 G109 D237 D338 D339 H340
Binding residue
(residue number reindexed from 1)		G22 C24 G76 G77 D205 D305 D306 H307
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.17,Ki=683nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0046872 metal ion binding
GO:0070005 cysteine-type aminopeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0009401 phosphoenolpyruvate-dependent sugar phosphotransferase system
GO:0009636 response to toxic substance
GO:0043418 homocysteine catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5wdl, PDBe:5wdl, PDBj:5wdl
PDBsum5wdl
PubMed30085657
UniProtA6LE66

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