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- PDB-2oag: Crystal structure of human dipeptidyl peptidase IV (DPPIV) with p... -

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Basic information

Entry
Database: PDB / ID: 2oag
TitleCrystal structure of human dipeptidyl peptidase IV (DPPIV) with pyrrolidine-constrained phenethylamine 29g
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine-peptidase / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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-DLI / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBackes, B.J. / Longenecker, K.L. / Hamilton, G.L. / Stewart, K.D. / Lai, C. / Kopecka, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Pyrrolidine-constrained phenethylamines: The design of potent, selective, and pharmacologically efficacious dipeptidyl peptidase IV (DPP4) inhibitors from a lead-like screening hit.
Authors: Backes, B.J. / Longenecker, K. / Hamilton, G.L. / Stewart, K. / Lai, C. / Kopecka, H. / von Geldern, T.W. / Madar, D.J. / Pei, Z. / Lubben, T.H. / Zinker, B.A. / Tian, Z. / Ballaron, S.J. / ...Authors: Backes, B.J. / Longenecker, K. / Hamilton, G.L. / Stewart, K. / Lai, C. / Kopecka, H. / von Geldern, T.W. / Madar, D.J. / Pei, Z. / Lubben, T.H. / Zinker, B.A. / Tian, Z. / Ballaron, S.J. / Stashko, M.A. / Mika, A.K. / Beno, D.W. / Kempf-Grote, A.J. / Black-Schaefer, C. / Sham, H.L. / Trevillyan, J.M.
History
DepositionDec 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Dec 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
B: Dipeptidyl peptidase 4
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,4585
Polymers337,0094
Non-polymers4481
Water59,7203315
1
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,9533
Polymers168,5052
Non-polymers4481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4


Theoretical massNumber of molelcules
Total (without water)168,5052
Polymers168,5052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.006, 126.225, 127.563
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.9999, -0.0112, 0.0031), (0.0108, -0.7932, 0.6089), (-0.0044, 0.6089, 0.7932)174.4428, -1.514, 0.7045
DetailsThe two protein dimers of the asymmetric unit are thought to be biologically relevant

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Components

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


Mass: 84252.336 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-DLI / (3R,4S)-1-{6-[3-(METHYLSULFONYL)PHENYL]PYRIMIDIN-4-YL}-4-(2,4,5-TRIFLUOROPHENYL)PYRROLIDIN-3-AMINE


Mass: 448.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H19F3N4O2S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3315 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
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: 2.3→50 Å / Num. obs: 163600 / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.108 / Χ2: 1.099 / Net I/σ(I): 6.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.3830.491154090.637192.3
2.38-2.483.30.438157640.656194.5
2.48-2.593.40.347159200.667195.4
2.59-2.733.50.267161690.689196.5
2.73-2.93.50.205163910.72198.1
2.9-3.123.60.149165960.865199.3
3.12-3.443.70.113167691.073199.9
3.44-3.933.80.09167831.4381100
3.93-4.953.90.075168121.9931100
4.95-503.80.059169871.747199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / FOM work R set: 0.839 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.24 8153 4.9 %
Rwork0.197 --
obs-163215 97.5 %
Displacement parametersBiso mean: 39.458 Å2
Baniso -1Baniso -2Baniso -3
1-4.513 Å20 Å2-1.184 Å2
2--0.306 Å20 Å2
3----4.819 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23796 0 31 3315 27142
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
2.3-2.320.3211380.30627032841
2.32-2.330.3851570.30429093066
2.33-2.350.3761540.30629133067
2.35-2.360.3371410.29630033144
2.36-2.380.3191540.27829373091
2.38-2.40.3421600.27829773137
2.4-2.420.3681640.28229553119
2.42-2.440.3231640.27329953159
2.44-2.460.2921760.26730263202
2.46-2.480.3031460.26629793125
2.48-2.50.3381420.25730743216
2.5-2.520.2811570.24230113168
2.52-2.540.2781560.2530183174
2.54-2.570.2761720.23530363208
2.57-2.590.271560.23230043160
2.59-2.620.2981420.23430503192
2.62-2.640.2891720.23630583230
2.64-2.670.3011750.22630793254
2.67-2.70.2381700.22130343204
2.7-2.730.2741610.22430843245
2.73-2.760.2831740.21930823256
2.76-2.790.2621550.22131013256
2.79-2.820.2821780.22230653243
2.82-2.860.2721680.20931443312
2.86-2.90.3261380.21331643302
2.9-2.940.2641620.20931743336
2.94-2.980.2761640.20631083272
2.98-3.020.2531630.20531743337
3.02-3.070.2631600.19431653325
3.07-3.120.2411850.19931333318
3.12-3.180.2351550.19731873342
3.18-3.230.2451460.19532393385
3.23-3.30.241780.19731363314
3.3-3.360.261860.19631663352
3.36-3.440.2781580.20231873345
3.44-3.520.2051690.19431943363
3.52-3.60.251720.19731613333
3.6-3.70.2331790.18431663345
3.7-3.810.2421720.17931913363
3.81-3.930.2091500.17132003350
3.93-4.070.2021680.16831983366
4.07-4.240.2021670.15832103377
4.24-4.430.1621660.13831643330
4.43-4.660.1791510.13832053356
4.66-4.950.1731880.14331853373
4.95-5.340.1651930.15731883381
5.34-5.870.1991690.16731983367
5.87-6.720.2131550.19132443399
6.72-8.460.2371560.20332503406
8.46-500.2241710.19932383409
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION3lig.par

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