Structure of PDB 2gbg Chain A Binding Site BS01

Receptor Information

>2gbg Chain A (length=730) Species: 10116 (Rattus norvegicus)

RRTYTLADYLKNTFRVKSYSLRWVSDSEYLYKQENNILLFNAEHGNSSIF
LENSTFEIFGDSISDYSVSPDRLFVLLEYNYVKQWRHSYTASYSIYDLNK
RQLITEEKIPNNTQWITWSQEGHKLAYVWKNDIYVKIEPHLPSHRITSTG
KENVIFNGINDWVYEEEIFGAYSALWWSPNGTFLAYAQFNDTGVPLIEYS
FYSDESLQYPKTVWIPYPKAGAVNPTVKFFIVNTDSLSSTTTTIPMQITA
PASVTTGDHYLCDVAWVSEDRISLQWLRRIQNYSVMAICDYDKTTLVWNC
PTTQEHIETSATGWCGRFRPAEPHFTSDGSSFYKIVSDKDGYKHICQFQK
DRKPEQVCTFITKGAWEVISIEALTSDYLYYISNEYKEMPGGRNLYKIQL
TDHTNKKCLSCDLNPERCQYYSVSLSKEAKYYQLGCRGPGLPLYTLHRST
DQKELRVLEDNSALDKMLQDVQMPSKKLDFIVLNETRFWYQMILPPHFDK
SKKYPLLIDVYAGPCSQKADAAFRLNWATYLASTENIIVASFDGRGSGYQ
GDKIMHAINKRLGTLEVEDQIEAARQFLKMGFVDSKRVAIWGWSYGGYVT
SMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNS
TVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDAGVDFQAMWYT
DEDHGIASSTAHQHIYSHMSHFLQQCFSLR

Ligand information

• Ligand ID: 1AD
• InChI: InChI=1S/C15H25N3O/c1-2-5-12-8-9-13(10-16)18(12)15(19)14(17)11-6-3-4-7-11/h11-14H,3-4,6-10,16-17H2,1H3/t12-,13-,14-/m0/s1
• InChIKey: RIKCMKYTGBHVSX-IHRRRGAJSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC#C[C@H]1CC[C@H](N1C(=O)[C@H](C2CCCC2)N)CN
  OpenEye OEToolkits 1.5.0: CC#CC1CCC(N1C(=O)C(C2CCCC2)N)CN
  CACTVS 3.341: CC#C[CH]1CC[CH](CN)N1C(=O)[CH](N)C2CCCC2
  CACTVS 3.341: CC#C[C@H]1CC[C@@H](CN)N1C(=O)[C@@H](N)C2CCCC2
  ACDLabs 10.04: O=C(N1C(C#CC)CCC1CN)C(N)C2CCCC2
• Formula: C15 H25 N3 O
• Name: (1S)-2-[(2S,5R)-2-(AMINOMETHYL)-5-PROP-1-YN-1-YLPYRROLIDIN-1-YL]-1-CYCLOPENTYL-2-OXOETHANAMINE
• DrugBank: DB06880
• ZINC: ZINC000036470909
• PDB chain: 2gbg Chain A Residue 768

Receptor-Ligand Complex Structure

Structure summary

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• PDB: 2gbg Crystal Structures of DPP-IV (CD26) from Rat Kidney Exhibit Flexible Accommodation of Peptidase-Selective Inhibitors.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): E203 E204 F355 Y548 S631 Y632 Y663 Y667
• Binding residue (residue number reindexed from 1): E166 E167 F318 Y511 S594 Y595 Y626 Y630
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.25,Ki=56nM

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

External links

• PDB: RCSB:2gbg, PDBe:2gbg, PDBj:2gbg
• PDBsum: 2gbg
• PubMed: 16768443
• UniProt: P14740|DPP4_RAT Dipeptidyl peptidase 4 (Gene Name=Dpp4)

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