Structure of PDB 3ccc Chain B Binding Site BS01

Receptor Information
>3ccc Chain B (length=724) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQNILVFNAEYGNSSVFLEN
STFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQL
ITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKED
IIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYS
DESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPAS
MLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVA
RQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKK
DCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKV
TCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLR
VLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPL
LLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMH
AINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGS
GSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRA
ENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGI
ASSTAHQHIYTHMSHFIKQCFSLP
Ligand information
Ligand ID7AC
InChIInChI=1S/C16H13ClN4/c1-21-9-20-14-6-10(7-18)15(12(8-19)16(14)21)11-4-2-3-5-13(11)17/h2-6,9H,8,19H2,1H3
InChIKeyYJLVMTVZVJSNHG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc3ccccc3c1c(C#N)cc2ncn(c2c1CN)C
OpenEye OEToolkits 1.5.0Cn1cnc2c1c(c(c(c2)C#N)c3ccccc3Cl)CN
CACTVS 3.341Cn1cnc2cc(C#N)c(c(CN)c12)c3ccccc3Cl
FormulaC16 H13 Cl N4
Name7-(aminomethyl)-6-(2-chlorophenyl)-1-methyl-1H-benzimidazole-5-carbonitrile
ChEMBLCHEMBL272114
DrugBankDB07239
ZINCZINC000029125222
PDB chain3ccc Chain B Residue 800 [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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PDB3ccc Structure-based design and synthesis of benzimidazole derivatives as dipeptidyl peptidase IV inhibitors.
Resolution2.71 Å
Binding residue
(original residue number in PDB)		E205 E206 S630 Y631 Y662 Y666 H740
Binding residue
(residue number reindexed from 1)		E163 E164 S588 Y589 Y620 Y624 H698
Annotation score1
Binding affinityBindingDB: IC50=8nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y547 S630 Y631 D708 H740
Catalytic site (residue number reindexed from 1) Y505 S588 Y589 D666 H698
Enzyme Commision number 3.4.14.5: dipeptidyl-peptidase IV.
Gene Ontology
Molecular Function
GO:0001618 virus receptor activity
GO:0002020 protease binding
GO:0004177 aminopeptidase activity
GO:0004252 serine-type endopeptidase activity
GO:0005102 signaling receptor binding
GO:0005515 protein binding
GO:0008236 serine-type peptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0045499 chemorepellent activity
Biological Process
GO:0001662 behavioral fear response
GO:0001666 response to hypoxia
GO:0006508 proteolysis
GO:0007155 cell adhesion
GO:0008284 positive regulation of cell population proliferation
GO:0010716 negative regulation of extracellular matrix disassembly
GO:0016486 peptide hormone processing
GO:0019065 receptor-mediated endocytosis of virus by host cell
GO:0031295 T cell costimulation
GO:0033632 regulation of cell-cell adhesion mediated by integrin
GO:0035641 locomotory exploration behavior
GO:0036343 psychomotor behavior
GO:0042110 T cell activation
GO:0043542 endothelial cell migration
GO:0046718 symbiont entry into host cell
GO:0046813 receptor-mediated virion attachment to host cell
GO:0050919 negative chemotaxis
GO:0061025 membrane fusion
GO:0090024 negative regulation of neutrophil chemotaxis
GO:0120116 glucagon processing
Cellular Component
GO:0005576 extracellular region
GO:0005765 lysosomal membrane
GO:0005886 plasma membrane
GO:0005925 focal adhesion
GO:0009986 cell surface
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030027 lamellipodium
GO:0030139 endocytic vesicle
GO:0031258 lamellipodium membrane
GO:0042995 cell projection
GO:0045121 membrane raft
GO:0046581 intercellular canaliculus
GO:0070062 extracellular exosome
GO:0070161 anchoring junction

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ccc, PDBe:3ccc, PDBj:3ccc
PDBsum3ccc
PubMed18346892
UniProtP27487|DPP4_HUMAN Dipeptidyl peptidase 4 (Gene Name=DPP4)

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