Structure of PDB 3eq9 Chain A Binding Site BS01

Receptor Information
>3eq9 Chain A (length=708) Species: 9823 (Sus scrofa) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFQYPDVYRDETAIQDYHGHKVCDPYAWLEDPDSEQTKAFVEAQNKITVP
FLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYV
QDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVT
IKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNAYPQQDGKSDGTET
STNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIR
EGCDPVNRLWYCDLQQESNGITGILKWVKLIDNFEGEYDYVTNEGTVFTF
KTNRHSPNYRLINIDFTDPEESKWKVLVPEHEKDVLEWVACVRSNFLVLC
YLHDVKNTLQLHDLATGALLKIFPLEVGSVVGYSGQKKDTEIFYQFTSFL
SPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPM
FIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGVLAVA
NIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTING
GSNGGLLVATCANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCS
DSKQHFEWLIKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKF
IATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIAR
CLNIDWIP
Ligand information
Ligand IDX97
InChIInChI=1S/C28H32N4O4/c33-24(31-19-9-15-23(31)25(34)30-17-7-8-18-30)16-10-20-32-26(35)28(29-27(32)36,21-11-3-1-4-12-21)22-13-5-2-6-14-22/h1-6,11-14,23H,7-10,15-20H2,(H,29,36)/t23-/m0/s1
InChIKeyPHYVMRFCTLZIHY-QHCPKHFHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1ccc(cc1)C2(C(=O)N(C(=O)N2)CCCC(=O)N3CCC[C@H]3C(=O)N4CCCC4)c5ccccc5
ACDLabs 12.01O=C(N1CCCC1)C5N(C(=O)CCCN4C(=O)C(c2ccccc2)(c3ccccc3)NC4=O)CCC5
CACTVS 3.370O=C(CCCN1C(=O)NC(C1=O)(c2ccccc2)c3ccccc3)N4CCC[CH]4C(=O)N5CCCC5
CACTVS 3.370O=C(CCCN1C(=O)NC(C1=O)(c2ccccc2)c3ccccc3)N4CCC[C@H]4C(=O)N5CCCC5
OpenEye OEToolkits 1.7.0c1ccc(cc1)C2(C(=O)N(C(=O)N2)CCCC(=O)N3CCCC3C(=O)N4CCCC4)c5ccccc5
FormulaC28 H32 N4 O4
Name3-{4-oxo-4-[(2S)-2-(pyrrolidin-1-ylcarbonyl)pyrrolidin-1-yl]butyl}-5,5-diphenylimidazolidine-2,4-dione
ChEMBLCHEMBL516159
DrugBank
ZINCZINC000040861032
PDB chain3eq9 Chain A Residue 711 [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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PDB3eq9 Prolyl oligopeptidase inhibition by N-acyl-pro-pyrrolidine-type molecules
Resolution2.47 Å
Binding residue
(original residue number in PDB)		F173 M235 R252 G254 C255 F476 S554 W595 R643 V644
Binding residue
(residue number reindexed from 1)		F171 M233 R250 G252 C253 F474 S552 W593 R641 V642
Annotation score1
Binding affinityMOAD: ic50=41nM
PDBbind-CN: -logKd/Ki=7.39,IC50=41nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y473 S554 D641 H680
Catalytic site (residue number reindexed from 1) Y471 S552 D639 H678
Enzyme Commision number 3.4.21.26: prolyl oligopeptidase.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0008236 serine-type peptidase activity
GO:0070012 oligopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3eq9, PDBe:3eq9, PDBj:3eq9
PDBsum3eq9
PubMed19006380
UniProtP23687|PPCE_PIG Prolyl endopeptidase (Gene Name=PREP)

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