Structure of PDB 4dtt Chain A Binding Site BS02

Receptor Information
>4dtt Chain A (length=956) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNPAIKRIGNHITKSPEDKREYRGLELANGIKVLLISDPTTDKSSAALDV
HIGSLSDPPNIAGLSHFLEHMLFLGTKKYPKENEYSQFLSEHAGSSNAFT
SGEHTNYYFDVSHEHLEGALDRFAQFFLSPLFDESAKDREVNAVDSEHEK
NVMNDAWRLFQLEKATGNPKHPFSKFGTGNKYTLETRPNQEGIDVRQELL
KFHSAYYSSNLMAVVVLGRESLDDLTNLVVKLFSEVENKNVPLPEFPEHP
FQEEHLKQLYKIVPIKDIRNLYVTFPIPDLQKYYKSNPGHYLGHLIGHEG
PGSLLSELKSKGWVNTLVGGQKEGARGFMFFIINVDLTEEGLLHVEDIIL
HMFQYIQKLRAEGPQEWVFQELKDLNAVAFRFKDKERPRGYTSKIAGILH
YYPLEEVLTAEYLLEEFRPDLIEMVLDKLRPENVRVAIVSKSFEGKTDRT
EEWYGTQYKQEAIPDEVIKKWQNADLNGKFKLPTKNEFIPTNFEILPLEK
EATPYPALIKDTAMSKLWFKQDDKFFLPKANLNFEFFSPFAYVDPLHSNM
AYLYLELLKDSLNEYAYAAELAGLSYDLQNTIYGMYLSVKGYNDKQPILL
KKIIEKMATFEIDEKRFEIIKEAYMRSLNNFRAEQPHQHAMYYLRLLMTE
VAWTKDELKEALDDVTLPRLKAFIPQLLSRLHIEALLHGNITKQAALGIM
QMVEDTLIEHAHTKPLLPSQLVRYREVQLPDRGWFVYQQRNEVHNNSGIE
IYYQTDMQSTSENMFLELFAQIISEPAFNTLRTKEQLGYIVFSGPRRANG
IQGLRFIIQSEKPPHYLESRVEAFLITMEKSIEDMTEEAFQKHIQALAIR
RLDKPKKLSAESAKYWGEIISQQYNFDRDNTEVAYLKTLTKEDIIKFYKE
MLAVDAPRRHKVSVHVLAREMDINLSQAPALPQPEVIQNMTEFKRGLPLF
PLVKPH
Ligand information
Ligand IDI41
InChIInChI=1S/C18H22N4O5/c1-27-18(26)15(7-14-8-19-12-20-14)21-16(23)10-22(11-17(24)25)9-13-5-3-2-4-6-13/h2-6,8,12,15H,7,9-11H2,1H3,(H,19,20)(H,21,23)(H,24,25)/t15-/m0/s1
InChIKeyVJXRDRMNYWCCEG-HNNXBMFYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352COC(=O)[CH](Cc1[nH]cnc1)NC(=O)CN(CC(O)=O)Cc2ccccc2
OpenEye OEToolkits 1.6.1COC(=O)C(Cc1cnc[nH]1)NC(=O)CN(Cc2ccccc2)CC(=O)O
OpenEye OEToolkits 1.6.1COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@](Cc2ccccc2)CC(=O)O
CACTVS 3.352COC(=O)[C@H](Cc1[nH]cnc1)NC(=O)CN(CC(O)=O)Cc2ccccc2
FormulaC18 H22 N4 O5
Name2-[[2-[[(2S)-3-(3H-IMIDAZOL-4-YL)-1-METHOXY-1-OXO-PROPAN-2-YL]AMINO]-2-OXO-ETHYL]-(PHENYLMETHYL)AMINO]ETHANOIC ACID;
COMPOUND 41367
ChEMBLCHEMBL3235412
DrugBank
ZINCZINC000095921296
PDB chain4dtt Chain A Residue 1102 [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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PDB4dtt Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-beta hydrolysis.
Resolution3.22 Å
Binding residue
(original residue number in PDB)		S138 N139 A140 E189 Y831
Binding residue
(residue number reindexed from 1)		S96 N97 A98 E147 Y789
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.54,IC50=2.9uM
Enzymatic activity
Catalytic site (original residue number in PDB) E111
Catalytic site (residue number reindexed from 1) E69
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

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:4dtt, PDBe:4dtt, PDBj:4dtt
PDBsum4dtt
PubMed24735644
UniProtP14735|IDE_HUMAN Insulin-degrading enzyme (Gene Name=IDE)

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