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- PDB-2ogz: Crystal structure of DPP-IV complexed with Lilly aryl ketone inhibitor -

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Basic information

Entry
Database: PDB / ID: 2ogz
TitleCrystal structure of DPP-IV complexed with Lilly aryl ketone inhibitor
ComponentsDipeptidyl peptidase
KeywordsHYDROLASE / DIPEPTIDYL PEPTIDASE IV / CD26 / DPIV / DPP-IV / DPP4 / Serine Protease / 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 / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / 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 / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / T cell costimulation / T cell activation / serine-type peptidase activity / 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-U1N / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTimm, D.E.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Discovery of non-covalent dipeptidyl peptidase IV inhibitors which induce a conformational change in the active site.
Authors: Sheehan, S.M. / Mest, H.J. / Watson, B.M. / Klimkowski, V.J. / Timm, D.E. / Cauvin, A. / Parsons, S.H. / Shi, Q. / Canada, E.J. / Wiley, M.R. / Ruehter, G. / Evers, B. / Petersen, S. / ...Authors: Sheehan, S.M. / Mest, H.J. / Watson, B.M. / Klimkowski, V.J. / Timm, D.E. / Cauvin, A. / Parsons, S.H. / Shi, Q. / Canada, E.J. / Wiley, M.R. / Ruehter, G. / Evers, B. / Petersen, S. / Blaszczak, L.C. / Pulley, S.R. / Margolis, B.J. / Wishart, G.N. / Renson, B. / Hankotius, D. / Mohr, M. / Zechel, J.C. / Michael Kalbfleisch, J. / Dingess-Hammond, E.A. / Boelke, A. / Weichert, A.G.
History
DepositionJan 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)169,5824
Polymers168,9252
Non-polymers6572
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-16 kcal/mol
Surface area56580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.595, 122.304, 112.721
Angle α, β, γ (deg.)90.00, 100.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Dipeptidyl peptidase /


Mass: 84462.617 Da / Num. of mol.: 2 / Fragment: DPP-IV extracellular domain, residues 39-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Chemical ChemComp-U1N / 4-[(3R)-3-{[2-(4-FLUOROPHENYL)-2-OXOETHYL]AMINO}BUTYL]BENZAMIDE


Mass: 328.381 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H21FN2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.55 Å3/Da / Density % sol: 51.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: PEG4000, SODIUM ACETATE, pH 8, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 83477 / Num. obs: 83477 / % possible obs: 86.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.132 / Χ2: 1.172 / Net I/σ(I): 6.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.5 / Num. unique all: 5564 / Χ2: 1.092 / % possible all: 58.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Translation3.5 Å8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N1M

1n1m


Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4231 4.3 %random
Rwork0.233 ---
all0.233 83477 --
obs0.233 83448 84.4 %-
Displacement parametersBiso mean: 35.642 Å2
Baniso -1Baniso -2Baniso -3
1--5.265 Å20 Å29.462 Å2
2---0.149 Å20 Å2
3---5.414 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11912 0 48 554 12514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.409
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4UNK.par

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