Structure of PDB 4pf9 Chain A Binding Site BS01

Receptor Information
>4pf9 Chain A (length=959) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDV
HIGSLSDPPNIAGLSHFLQHMLFLGTKKYPKENEYSQFLSEHAGSSNAFT
SGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEK
NVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELL
KFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHP
FQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEG
PGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIIL
HMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILH
YYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRT
EEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEK
EATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNM
AYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILL
KKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTE
VAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIM
QMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIE
IYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANG
IQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIR
RLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKE
MLAVDAPRRHKVSVHVLAREMDSDINLSQAPALPQPEVIQNMTEFKRGLP
LFPLVKPHI
Ligand information
Ligand ID2Q6
InChIInChI=1S/C44H55N5O5/c1-53-44(52)47-30-36(28-32-27-35-14-7-8-16-40(35)46-29-32)33-19-23-38(24-20-33)54-26-9-3-4-11-31-17-21-37(22-18-31)48-42(50)41(34-12-5-2-6-13-34)49-25-10-15-39(45)43(49)51/h7-8,14,16-24,27,29,34,36,39,41H,2-6,9-13,15,25-26,28,30,45H2,1H3,(H,47,52)(H,48,50)/t36-,39+,41+/m1/s1
InChIKeyIGRIVAWLJUPVMM-UDEWTJCRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2COC(=O)NCC(Cc1cc2ccccc2nc1)c3ccc(cc3)OCCCCCc4ccc(cc4)NC(=O)C(C5CCCCC5)N6CCCC(C6=O)N
CACTVS 3.385COC(=O)NC[C@@H](Cc1cnc2ccccc2c1)c3ccc(OCCCCCc4ccc(NC(=O)[C@H](C5CCCCC5)N6CCC[C@H](N)C6=O)cc4)cc3
OpenEye OEToolkits 1.9.2COC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3ccc(cc3)OCCCCCc4ccc(cc4)NC(=O)[C@H](C5CCCCC5)N6CCC[C@@H](C6=O)N
ACDLabs 12.01O=C(OC)NCC(c4ccc(OCCCCCc1ccc(cc1)NC(=O)C(N2C(=O)C(N)CCC2)C3CCCCC3)cc4)Cc5cc6ccccc6nc5
CACTVS 3.385COC(=O)NC[CH](Cc1cnc2ccccc2c1)c3ccc(OCCCCCc4ccc(NC(=O)[CH](C5CCCCC5)N6CCC[CH](N)C6=O)cc4)cc3
FormulaC44 H55 N5 O5
Namemethyl [(2S)-2-[4-({5-[4-({(2S)-2-[(3S)-3-amino-2-oxopiperidin-1-yl]-2-cyclohexylacetyl}amino)phenyl]pentyl}oxy)phenyl]-3-(quinolin-3-yl)propyl]carbamate
ChEMBLCHEMBL4437643
DrugBank
ZINCZINC000230583416
PDB chain4pf9 Chain A Residue 1101 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4pf9 Dual Exosite-binding Inhibitors of Insulin-degrading Enzyme Challenge Its Role as the Primary Mediator of Insulin Clearance in Vivo.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		F202 E205 T208 Y302 Y314 H332 H336 G339 E341 L359 V360 G361 Q363 K364 I374 N376 R477 A479
Binding residue
(residue number reindexed from 1)		F160 E163 T166 Y260 Y272 H290 H294 G297 E299 L317 V318 G319 Q321 K322 I332 N334 R435 A437
Annotation score1
Binding affinityMOAD: ic50=4nM
BindingDB: IC50=4.0nM
Enzymatic activity
Catalytic site (original residue number in PDB) Q111
Catalytic site (residue number reindexed from 1) Q69
Enzyme Commision number 3.4.24.56: insulysin.
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0004175 endopeptidase activity
GO:0004222 metalloendopeptidase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0042277 peptide binding
GO:0042803 protein homodimerization activity
GO:0043559 insulin binding
GO:0046872 metal ion binding
Biological Process
GO:0006508 proteolysis
GO:0008286 insulin receptor signaling pathway
GO:0010815 bradykinin catabolic process
GO:0010992 ubiquitin recycling
GO:0019885 antigen processing and presentation of endogenous peptide antigen via MHC class I
GO:0030163 protein catabolic process
GO:0032092 positive regulation of protein binding
GO:0042447 hormone catabolic process
GO:0043171 peptide catabolic process
GO:0045732 positive regulation of protein catabolic process
GO:0046718 symbiont entry into host cell
GO:0050435 amyloid-beta metabolic process
GO:0051603 proteolysis involved in protein catabolic process
GO:0097242 amyloid-beta clearance
GO:0150094 amyloid-beta clearance by cellular catabolic process
GO:1901142 insulin metabolic process
GO:1901143 insulin catabolic process
GO:1903715 regulation of aerobic respiration
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005777 peroxisome
GO:0005782 peroxisomal matrix
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016323 basolateral plasma membrane
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pf9, PDBe:4pf9, PDBj:4pf9
PDBsum4pf9
PubMed26085101
UniProtP14735|IDE_HUMAN Insulin-degrading enzyme (Gene Name=IDE)

[Back to BioLiP]