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- PDB-5y7h: Crystal structure of human DPP4 in complex with inhibitor3 -

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Basic information

Entry
Database: PDB / ID: 5y7h
TitleCrystal structure of human DPP4 in complex with inhibitor3
ComponentsDipeptidyl peptidase 4
KeywordsHYDROLASE / DPP4 / inhibitor
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-8O3 / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLee, H.K. / Kim, E.E.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2017
Title: Unique binding mode of Evogliptin with human dipeptidyl peptidase IV.
Authors: Lee, H.K. / Kim, M.K. / Kim, H.D. / Kim, H.J. / Kim, J.W. / Lee, J.O. / Kim, C.W. / Kim, E.E.
History
DepositionAug 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,1866
Polymers168,9252
Non-polymers1,2614
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-16 kcal/mol
Surface area56350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.301, 126.420, 113.382
Angle α, β, γ (deg.)90.00, 100.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dipeptidyl peptidase 4 / ADABP / Adenosine deaminase complexing protein 2 / ADCP-2 / Dipeptidyl peptidase IV / DPP IV / T- ...ADABP / Adenosine deaminase complexing protein 2 / ADCP-2 / Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103


Mass: 84462.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Chemical
ChemComp-8O3 / (R)-4-(3-amino-4-(2,4,5-trifluorophenyl)butanoyl)piperazin-2-one


Mass: 315.291 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16F3N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20~28% (w/v) polyethylene glycol 4000, 0.1M HEPES or Tris pH 7.5~8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 35739 / % possible obs: 91.5 % / Redundancy: 2.1 % / Net I/σ(I): 18.25
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 4.19 / % possible all: 75.6

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X70

1x70


Resolution: 3→46.172 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 1650 5.05 %
Rwork0.1992 --
obs0.2015 32658 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11911 0 88 150 12149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00112357
X-RAY DIFFRACTIONf_angle_d0.41716818
X-RAY DIFFRACTIONf_dihedral_angle_d17.7077170
X-RAY DIFFRACTIONf_chiral_restr0.041760
X-RAY DIFFRACTIONf_plane_restr0.0022135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.08840.3572970.28612081X-RAY DIFFRACTION73
3.0884-3.18810.32611170.25512312X-RAY DIFFRACTION82
3.1881-3.3020.30771300.24772510X-RAY DIFFRACTION89
3.302-3.43420.27121460.23262537X-RAY DIFFRACTION90
3.4342-3.59040.26251320.20652571X-RAY DIFFRACTION91
3.5904-3.77960.25521480.20122621X-RAY DIFFRACTION92
3.7796-4.01630.24191330.18812603X-RAY DIFFRACTION92
4.0163-4.32620.20821460.16582662X-RAY DIFFRACTION95
4.3262-4.76110.19281360.15042739X-RAY DIFFRACTION97
4.7611-5.44910.18051430.15832762X-RAY DIFFRACTION97
5.4491-6.86170.22561500.20282782X-RAY DIFFRACTION98
6.8617-46.17790.26531720.21692828X-RAY DIFFRACTION98

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