Structure of PDB 3e4a Chain B Binding Site BS03

Receptor Information
>3e4a Chain B (length=961) 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
MLAVDAPRRHKVSVHVLAREMDSNPVVGNLSQAPALPQPEVIQNMTEFKR
GLPLFPLVKPH
Ligand information
Ligand IDQIX
InChIInChI=1S/C25H34N8O6/c26-20(34)13-30-22(36)14-31-24(38)19(6-3-9-29-25(27)28)32-23(37)18(12-21(35)33-39)11-15-7-8-16-4-1-2-5-17(16)10-15/h1-2,4-5,7-8,10,18-19,39H,3,6,9,11-14H2,(H2,26,34)(H,30,36)(H,31,38)(H,32,37)(H,33,35)(H4,27,28,29)/t18-,19+/m1/s1
InChIKeyNINUSDCYEXCHSI-MOPGFXCFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0[H]N=C(N)NCCCC(C(=O)NCC(=O)NCC(=O)N)NC(=O)C(Cc1ccc2ccccc2c1)CC(=O)NO
CACTVS 3.341NC(=N)NCCC[CH](NC(=O)[CH](CC(=O)NO)Cc1ccc2ccccc2c1)C(=O)NCC(=O)NCC(N)=O
CACTVS 3.341NC(=N)NCCC[C@H](NC(=O)[C@@H](CC(=O)NO)Cc1ccc2ccccc2c1)C(=O)NCC(=O)NCC(N)=O
ACDLabs 10.04O=C(N)CNC(=O)CNC(=O)C(NC(=O)C(CC(=O)NO)Cc2ccc1c(cccc1)c2)CCCNC(=[N@H])N
OpenEye OEToolkits 1.5.0[H]/N=C(/N)\NCCC[C@@H](C(=O)NCC(=O)NCC(=O)N)NC(=O)[C@H](Cc1ccc2ccccc2c1)CC(=O)NO
FormulaC25 H34 N8 O6
NameN~2~-[(2R)-4-(HYDROXYAMINO)-2-(2-NAPHTHYLMETHYL)-4-OXOBUTANOYL]-L-ARGINYLGLYCYLGLYCINAMIDE
ChEMBL
DrugBank
ZINCZINC000058638501
PDB chain3e4a Chain B Residue 2001 [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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PDB3e4a Designed inhibitors of insulin-degrading enzyme regulate the catabolism and activity of insulin.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		H108 Q111 H112 F115 L116 N139 E189 F820 R824 Y831
Binding residue
(residue number reindexed from 1)		H66 Q69 H70 F73 L74 N97 E147 F778 R782 Y789
Annotation score1
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:3e4a, PDBe:3e4a, PDBj:3e4a
PDBsum3e4a
PubMed20498699
UniProtP14735|IDE_HUMAN Insulin-degrading enzyme (Gene Name=IDE)

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