Structure of PDB 5kby Chain A

Receptor sequence
>5kbyA (length=725) Species: 9606 (Homo sapiens) [Search protein sequence]
RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQNILVFNAEYGNSSVFLE
NSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQ
LITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKE
DIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFY
SDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPA
SMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLV
ARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDK
KDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTK
VTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGL
RVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYP
LLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIM
HAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLG
SGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSR
AENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHG
IASSTAHQHIYTHMSHFIKQCFSLP
3D structure
PDB5kby Trelagliptin (SYR-472, Zafatek), Novel Once-Weekly Treatment for Type 2 Diabetes, Inhibits Dipeptidyl Peptidase-4 (DPP-4) via a Non-Covalent Mechanism.
ChainA
Resolution2.24 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) Y547 S630 Y631 D708 H740
Catalytic site (residue number reindexed from 1) Y506 S589 Y590 D667 H699
Enzyme Commision number 3.4.14.5: dipeptidyl-peptidase IV.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 6RL A E205 E206 Y547 S630 Y631 V656 W659 Y662 Y666 V711 E164 E165 Y506 S589 Y590 V615 W618 Y621 Y625 V670 MOAD: Ki=1.5nM
PDBbind-CN: -logKd/Ki=8.82,Ki=1.5nM
BindingDB: IC50=1.3nM,Ki=5.1nM
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
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Cellular Component
External links
PDB RCSB:5kby, PDBe:5kby, PDBj:5kby
PDBsum5kby
PubMed27328054
UniProtP27487|DPP4_HUMAN Dipeptidyl peptidase 4 (Gene Name=DPP4)

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