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- PDB-2oqi: Human Dipeptidyl Peptidase IV (DPP4) with Piperidinone-constraine... -

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Basic information

Entry
Database: PDB / ID: 2oqi
TitleHuman Dipeptidyl Peptidase IV (DPP4) with Piperidinone-constrained phenethylamine
ComponentsDipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
KeywordsHYDROLASE / serine-peptidase / 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-GGO / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPei, Z. / Li, X. / von Geldern, T.W. / Longenecker, K.L. / Pireh, D. / Stewart, K.D. / Backes, B.J. / Lai, C. / Lubben, T.H. / Ballaron, S.J. ...Pei, Z. / Li, X. / von Geldern, T.W. / Longenecker, K.L. / Pireh, D. / Stewart, K.D. / Backes, B.J. / Lai, C. / Lubben, T.H. / Ballaron, S.J. / Beno, D.W. / Kempf-Grote, A.J. / Sham, H.L. / Trevillyan, J.M.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Discovery and Structure-Activity Relationships of Piperidinone- and Piperidine-Constrained Phenethylamines as Novel, Potent, and Selective Dipeptidyl Peptidase IV Inhibitors.
Authors: Pei, Z. / Li, X. / Geldern, T.W. / Longenecker, K. / Pireh, D. / Stewart, K.D. / Backes, B.J. / Lai, C. / Lubben, T.H. / Ballaron, S.J. / Beno, D.W. / Kempf-Grote, A.J. / Sham, H.L. / Trevillyan, J.M.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
C: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
D: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,2435
Polymers337,8504
Non-polymers3921
Water0
1
A: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,3183
Polymers168,9252
Non-polymers3921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-13 kcal/mol
Surface area56760 Å2
MethodPISA
2
C: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)
D: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV) (T-cell activation antigen CD26) (TP103) (Adenosine deaminase complexing protein 2) (ADABP)


Theoretical massNumber of molelcules
Total (without water)168,9252
Polymers168,9252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-19 kcal/mol
Surface area57070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.294, 127.300, 126.799
Angle α, β, γ (deg.)90.000, 96.450, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biologically relevant assembly is thought to consist of a dimer, and the asymmetric unit contains two of these dimers.

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Components

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


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: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Chemical ChemComp-GGO / (4R,5R)-5-AMINO-1-[2-(1,3-BENZODIOXOL-5-YL)ETHYL]-4-(2,4,5-TRIFLUOROPHENYL)PIPERIDIN-2-ONE


Mass: 392.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19F3N2O3

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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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 86018 / % possible obs: 89.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.1 / Χ2: 1.169 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.92.30.37478210.71582.4
2.9-3.022.50.30580490.77684.5
3.02-3.152.60.24981270.85685.4
3.15-3.322.80.19182090.92386.1
3.32-3.532.90.1582741.04386.7
3.53-3.83.10.11683481.12187.7
3.8-4.183.20.09486851.25790.7
4.18-4.793.30.07892321.45296.5
4.79-6.033.60.07895621.39199.4
6.03-503.80.06197111.41999.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→50 Å / FOM work R set: 0.751 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.284 4148 4.5 %
Rwork0.239 --
obs-83542 90 %
Displacement parametersBiso mean: 33.817 Å2
Baniso -1Baniso -2Baniso -3
1-15.018 Å20 Å23.084 Å2
2---0.527 Å20 Å2
3----14.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23792 0 28 0 23820
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.820.417750.37412071282
2.82-2.840.363730.37414391512
2.84-2.860.447640.36214711535
2.86-2.880.466810.37614921573
2.88-2.90.443520.37514941546
2.9-2.920.362760.34814561532
2.92-2.940.375790.34715001579
2.94-2.970.431890.34414801569
2.97-2.990.381590.32615161575
2.99-3.020.398720.34114931565
3.02-3.040.451800.3214831563
3.04-3.070.391850.31114761561
3.07-3.10.393880.3215751663
3.1-3.120.325780.28814441522
3.12-3.150.311850.29315281613
3.15-3.180.35830.29415031586
3.18-3.220.327630.28114991562
3.22-3.250.287910.27815241615
3.25-3.280.356730.28915231596
3.28-3.320.329870.28415121599
3.32-3.360.345980.27515121610
3.36-3.40.387760.2715231599
3.4-3.440.313860.2815311617
3.44-3.480.257780.2515181596
3.48-3.530.295860.26115651651
3.53-3.580.352690.27315161585
3.58-3.630.334860.25415651651
3.63-3.680.264820.2315051587
3.68-3.740.286990.21716021701
3.74-3.80.248640.22915481612
3.8-3.870.271870.21815741661
3.87-3.940.266700.21716081678
3.94-4.010.26830.21616061689
4.01-4.090.238860.21716701756
4.09-4.180.261810.21516411722
4.18-4.280.287930.20216581751
4.28-4.390.233820.18217141796
4.39-4.50.224910.17717111802
4.5-4.640.205820.17117161798
4.64-4.790.2311010.17617341835
4.79-4.960.205960.18317651861
4.96-5.160.2191050.18517331838
5.16-5.390.2111040.18617451849
5.39-5.670.24940.19917681862
5.67-6.030.256990.217881887
6.03-6.490.234680.20417761844
6.49-7.150.258940.22818001894
7.15-8.180.263880.20117791867
8.18-10.290.238740.19118261900
10.29-500.2671130.25117821895
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2lig.par

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