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- PDB-5y7k: Crystal structure of human DPP4 in complex with inhibitor1 -

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Basic information

Entry
Database: PDB / ID: 5y7k
TitleCrystal structure of human DPP4 in complex with inhibitor1
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE / DPP4 / inhibitor
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / virus receptor activity / lamellipodium / 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 / signaling receptor binding / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Alpha/Beta hydrolase fold, catalytic domain ...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-8VU / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.512 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
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)339,4568
Polymers337,8504
Non-polymers1,6064
Water4,900272
1
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7284
Polymers168,9252
Non-polymers8032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-16 kcal/mol
Surface area57370 Å2
MethodPISA
2
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7284
Polymers168,9252
Non-polymers8032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-16 kcal/mol
Surface area57120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.365, 131.920, 123.409
Angle α, β, γ (deg.)90.00, 89.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dipeptidyl peptidase 4 / 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.: 4
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-8VU / (R)-4-((R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl)-3-(tert-butoxymethyl)piperazine-2-one / Evogliptin


Mass: 401.423 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26F3N3O3 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
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
PH range: 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 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.512→41.136 Å / Num. obs: 129816 / % possible obs: 97.7 % / Redundancy: 2.8 % / Net I/σ(I): 14.1
Reflection shellResolution: 2.52→2.61 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.07 / % possible all: 92.3

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Processing

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

1x70


Resolution: 2.512→41.136 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 6379 5.03 %
Rwork0.2054 --
obs0.2072 126777 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.512→41.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23820 0 112 272 24204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224642
X-RAY DIFFRACTIONf_angle_d0.46333538
X-RAY DIFFRACTIONf_dihedral_angle_d18.57214342
X-RAY DIFFRACTIONf_chiral_restr0.0413517
X-RAY DIFFRACTIONf_plane_restr0.0024257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5119-2.54050.31231840.29013271X-RAY DIFFRACTION79
2.5405-2.57040.32482180.28513802X-RAY DIFFRACTION94
2.5704-2.60170.3332070.29823879X-RAY DIFFRACTION94
2.6017-2.63460.35382120.28453876X-RAY DIFFRACTION95
2.6346-2.66930.27742030.25893895X-RAY DIFFRACTION95
2.6693-2.70580.29142190.25663946X-RAY DIFFRACTION96
2.7058-2.74450.32112060.25033947X-RAY DIFFRACTION96
2.7445-2.78540.28382230.24533912X-RAY DIFFRACTION96
2.7854-2.8290.27971810.24673974X-RAY DIFFRACTION96
2.829-2.87530.29652170.24693999X-RAY DIFFRACTION97
2.8753-2.92490.28782310.24683999X-RAY DIFFRACTION98
2.9249-2.97810.29082010.24654020X-RAY DIFFRACTION98
2.9781-3.03530.28362200.24234019X-RAY DIFFRACTION98
3.0353-3.09730.28012120.22694042X-RAY DIFFRACTION98
3.0973-3.16460.2572380.23594074X-RAY DIFFRACTION99
3.1646-3.23820.2931990.23454109X-RAY DIFFRACTION99
3.2382-3.31910.27681980.23134081X-RAY DIFFRACTION99
3.3191-3.40880.27042360.23344044X-RAY DIFFRACTION99
3.4088-3.50910.25832160.22174087X-RAY DIFFRACTION99
3.5091-3.62230.26122030.21134126X-RAY DIFFRACTION99
3.6223-3.75170.24332010.19454107X-RAY DIFFRACTION99
3.7517-3.90180.23032050.19054096X-RAY DIFFRACTION100
3.9018-4.07920.20472090.17354116X-RAY DIFFRACTION100
4.0792-4.2940.16622090.16124124X-RAY DIFFRACTION100
4.294-4.56270.18412030.14944145X-RAY DIFFRACTION100
4.5627-4.91450.1722010.144170X-RAY DIFFRACTION100
4.9145-5.40810.1682550.1474103X-RAY DIFFRACTION100
5.4081-6.18840.21092210.1684122X-RAY DIFFRACTION100
6.1884-7.78810.21532250.19184166X-RAY DIFFRACTION100
7.7881-41.14180.24782260.21744147X-RAY DIFFRACTION98

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