Structure of PDB 1wm1 Chain A Binding Site BS01

Receptor Information
>1wm1 Chain A (length=313) Species: 615 (Serratia marcescens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRGLYPPLAAYDSGWLDTGDGHRIYWELSGNPNGKPAVFIHGGPGGGISP
HHRQLFDPERYKVLLFDQRGCGRSRPHASLDNNTTWHLVADIERLREMAG
VEQWLVFGGSWGSTLALAYAQTHPERVSEMVLRGIFTLRKQRLHWYYQDG
ASRFFPEKWERVLSILSDDERKDVIAAYRQRLTSADPQVQLEAAKLWSVW
EGETVTLLPSRESASFGEDDFALAFARIENHYFTHLGFLESDDQLLRNVP
LIRHIPAVIVHGRYDMACQVQNAWDLAKAWPEAELHIVEGAGHSYDEPGI
LHQLMIATDRFAG
Ligand information
Ligand IDPTB
InChIInChI=1S/C11H17N3O2/c1-11(2,3)10-14-13-9(16-10)8(15)7-5-4-6-12-7/h7,12H,4-6H2,1-3H3/t7-/m0/s1
InChIKeyYUKGJYBQODPVBL-ZETCQYMHSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)(C)c1oc(nn1)C(=O)[CH]2CCCN2
CACTVS 3.341CC(C)(C)c1oc(nn1)C(=O)[C@@H]2CCCN2
OpenEye OEToolkits 1.5.0CC(C)(C)c1nnc(o1)C(=O)[C@@H]2CCCN2
OpenEye OEToolkits 1.5.0CC(C)(C)c1nnc(o1)C(=O)C2CCCN2
ACDLabs 10.04O=C(c1nnc(o1)C(C)(C)C)C2NCCC2
FormulaC11 H17 N3 O2
Name(5-TERT-BUTYL-1,3,4-OXADIAZOL-2-YL)[(2R)-PYRROLIDIN-2-YL]METHANONE;
2-PROLYL-5-TERT-BUTYL-[1,3,4]OXADIAZOLE
ChEMBLCHEMBL403772
DrugBankDB03833
ZINCZINC000005950679
PDB chain1wm1 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1wm1 Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G45 G46 S113 W114 R136 F139 E204 E232 F236 H296
Binding residue
(residue number reindexed from 1)		G42 G43 S110 W111 R133 F136 E201 E229 F233 H293
Annotation score1
Binding affinityMOAD: Ki=0.5uM
PDBbind-CN: -logKd/Ki=6.30,Ki=0.5uM
BindingDB: Ki=500nM
Enzymatic activity
Catalytic site (original residue number in PDB) G46 S113 W114 D268 H296
Catalytic site (residue number reindexed from 1) G43 S110 W111 D265 H293
Enzyme Commision number 3.4.11.5: prolyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0008233 peptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1wm1, PDBe:1wm1, PDBj:1wm1
PDBsum1wm1
PubMed12893291
UniProtO32449|PIP_SERMA Proline iminopeptidase (Gene Name=pip)

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