Structure of PDB 2gbi Chain A Binding Site BS01

Receptor Information
>2gbi Chain A (length=730) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RRTYTLADYLKNTFRVKSYSLRWVSDSEYLYKQENNILLFNAEHGNSSIF
LENSTFEIFGDSISDYSVSPDRLFVLLEYNYVKQWRHSYTASYSIYDLNK
RQLITEEKIPNNTQWITWSQEGHKLAYVWKNDIYVKIEPHLPSHRITSTG
KENVIFNGINDWVYEEEIFGAYSALWWSPNGTFLAYAQFNDTGVPLIEYS
FYSDESLQYPKTVWIPYPKAGAVNPTVKFFIVNTDSLSSTTTTIPMQITA
PASVTTGDHYLCDVAWVSEDRISLQWLRRIQNYSVMAICDYDKTTLVWNC
PTTQEHIETSATGWCGRFRPAEPHFTSDGSSFYKIVSDKDGYKHICQFQK
DRKPEQVCTFITKGAWEVISIEALTSDYLYYISNEYKEMPGGRNLYKIQL
TDHTNKKCLSCDLNPERCQYYSVSLSKEAKYYQLGCRGPGLPLYTLHRST
DQKELRVLEDNSALDKMLQDVQMPSKKLDFIVLNETRFWYQMILPPHFDK
SKKYPLLIDVYAGPCSQKADAAFRLNWATYLASTENIIVASFDGRGSGYQ
GDKIMHAINKRLGTLEVEDQIEAARQFLKMGFVDSKRVAIWGWSYGGYVT
SMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNS
TVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDAGVDFQAMWYT
DEDHGIASSTAHQHIYSHMSHFLQQCFSLR
Ligand information
Ligand IDXIH
InChIInChI=1S/C20H23N7O2/c1-24-17-16(18(28)25(2)20(24)29)27(11-14-7-4-3-6-13(14)10-21)19(23-17)26-9-5-8-15(22)12-26/h3-4,6-7,15H,5,8-9,11-12,22H2,1-2H3/t15-/m1/s1
InChIKeyXJNKUWDMCBZMTG-OAHLLOKOSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04N#Cc1ccccc1Cn2c4c(nc2N3CCCC(N)C3)N(C(=O)N(C4=O)C)C
OpenEye OEToolkits 1.5.0CN1c2c(n(c(n2)N3CCC[C@H](C3)N)Cc4ccccc4C#N)C(=O)N(C1=O)C
OpenEye OEToolkits 1.5.0CN1c2c(n(c(n2)N3CCCC(C3)N)Cc4ccccc4C#N)C(=O)N(C1=O)C
CACTVS 3.341CN1C(=O)N(C)c2nc(N3CCC[CH](N)C3)n(Cc4ccccc4C#N)c2C1=O
CACTVS 3.341CN1C(=O)N(C)c2nc(N3CCC[C@@H](N)C3)n(Cc4ccccc4C#N)c2C1=O
FormulaC20 H23 N7 O2
Name2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE
ChEMBL
DrugBankDB08743
ZINCZINC000003839213
PDB chain2gbi Chain A Residue 901 [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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PDB2gbi Crystal Structures of DPP-IV (CD26) from Rat Kidney Exhibit Flexible Accommodation of Peptidase-Selective Inhibitors.
Resolution3.3 Å
Binding residue
(original residue number in PDB)		R123 E203 E204 Y548 S631 Y632 Y663 V712
Binding residue
(residue number reindexed from 1)		R86 E166 E167 Y511 S594 Y595 Y626 V675
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.52,Ki=3nM
BindingDB: Ki=3nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y548 S631 Y632 D709 H741
Catalytic site (residue number reindexed from 1) Y511 S594 Y595 D672 H704
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:0005518 collagen binding
GO:0008236 serine-type peptidase activity
GO:0008239 dipeptidyl-peptidase activity
GO:0042277 peptide binding
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:0002337 B-1a B cell differentiation
GO:0002709 regulation of T cell mediated immunity
GO:0002717 positive regulation of natural killer cell mediated immunity
GO:0006508 proteolysis
GO:0007155 cell adhesion
GO:0008284 positive regulation of cell population proliferation
GO:0010716 negative regulation of extracellular matrix disassembly
GO:0030163 protein catabolic process
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:0050919 negative chemotaxis
GO:0090024 negative regulation of neutrophil chemotaxis
Cellular Component
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0009986 cell surface
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:0070161 anchoring junction

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2gbi, PDBe:2gbi, PDBj:2gbi
PDBsum2gbi
PubMed16768443
UniProtP14740|DPP4_RAT Dipeptidyl peptidase 4 (Gene Name=Dpp4)

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