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- PDB-2i3z: rat DPP-IV with xanthine mimetic inhibitor #7 -

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Basic information

Entry
Database: PDB / ID: 2i3z
Titlerat DPP-IV with xanthine mimetic inhibitor #7
ComponentsDipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
KeywordsHYDROLASE / enzyme / peptidase / inhibitor
Function / homology
Function and homology information


B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus ...B-1a B cell differentiation / regulation of T cell mediated immunity / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / psychomotor behavior / chemorepellent activity / intercellular canaliculus / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / positive regulation of natural killer cell mediated immunity / dipeptidyl-peptidase activity / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / endothelial cell migration / behavioral fear response / aminopeptidase activity / collagen binding / T cell costimulation / serine-type peptidase activity / T cell activation / peptide binding / protein catabolic process / virus receptor activity / lamellipodium / protease binding / response to hypoxia / cell adhesion / membrane raft / apical plasma membrane / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / 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 ...Dipeptidyl peptidase 4, low complexity region / Dipeptidyl peptidase IV (DPP IV) low complexity region / 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-LIR / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKurukulasuriya, R. / Rohde, J.J. / Szczepankiewicz, B.G. / Basha, F. / Lai, C. / Winn, M. / Stewart, K.D. / Longenecker, K.L. / Lubben, T.W. / Ballaron, S.J. ...Kurukulasuriya, R. / Rohde, J.J. / Szczepankiewicz, B.G. / Basha, F. / Lai, C. / Winn, M. / Stewart, K.D. / Longenecker, K.L. / Lubben, T.W. / Ballaron, S.J. / Sham, H.L. / VonGeldern, T.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Xanthine mimetics as potent dipeptidyl peptidase IV inhibitors.
Authors: Kurukulasuriya, R. / Rohde, J.J. / Szczepankiewicz, B.G. / Basha, F. / Lai, C. / Jae, H.S. / Winn, M. / Stewart, K.D. / Longenecker, K.L. / Lubben, T.W. / Ballaron, S.J. / Sham, H.L. / von Geldern, T.W.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: 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 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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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)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,0413
Polymers168,6752
Non-polymers3651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-15 kcal/mol
Surface area56540 Å2
MethodPISA
2
A: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
hetero molecules

A: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
hetero molecules

A: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)507,1229
Polymers506,0256
Non-polymers1,0963
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area21600 Å2
ΔGint-90 kcal/mol
Surface area162380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.293, 207.293, 207.293
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
DetailsThe aymmetric unit consists of a dimer thought to be biologically relevant

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Components

#1: Protein Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)


Mass: 84337.578 Da / Num. of mol.: 2
Fragment: DIPEPTIDYL PEPTIDASE SOLUBLE FORM (RESIDUES 38-767)
Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P14740, dipeptidyl-peptidase IV
#2: Chemical ChemComp-LIR / 2-[(3S)-3-AMINOPIPERIDIN-1-YL]-1-(2-CYANOBENZYL)-5-METHYL-4,6-DIOXO-3,4,5,6-TETRAHYDROPYRROLO[3,4-D]IMIDAZOL-1-IUM


Mass: 365.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N6O2

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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: 4.4 Å3/Da / Density % sol: 72.04 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / 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: 2.9→50 Å / Num. obs: 65530 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.115 / Χ2: 1.155 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-36.30.57964710.44899.1
3-3.126.50.39764790.4899.2
3.12-3.276.60.27863950.55599.2
3.27-3.446.80.21665260.6799.7
3.44-3.657.10.1665640.87599.9
3.65-3.947.30.1365191.069100
3.94-4.337.40.10465721.368100
4.33-4.967.50.08665691.725100
4.96-6.247.50.08166361.621100
6.24-507.30.06167992.32499.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→20 Å / FOM work R set: 0.741 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.29 3294 5 %
Rwork0.253 --
obs-65257 99.6 %
Displacement parametersBiso mean: 47.574 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11840 0 27 0 11867
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
2.9-2.920.47550.46412211276
2.92-2.940.449650.4311931258
2.94-2.960.456590.45412591318
2.96-2.980.466750.42711581233
2.98-30.441570.40212591316
3-3.030.454530.40612141267
3.03-3.050.516630.40512391302
3.05-3.070.458690.38511991268
3.07-3.10.522580.36812451303
3.1-3.120.38730.33912311304
3.12-3.150.338750.34211931268
3.15-3.180.45760.34912361312
3.18-3.210.376580.3412031261
3.21-3.230.282740.32212391313
3.23-3.260.404590.33112361295
3.26-3.30.432590.33112341293
3.3-3.330.357550.31512281283
3.33-3.360.313700.31312271297
3.36-3.40.349620.3112551317
3.4-3.440.327680.31112261294
3.44-3.470.374600.31412351295
3.47-3.520.35490.30112461295
3.52-3.560.356720.29112261298
3.56-3.60.357620.2912231285
3.6-3.650.387560.27212611317
3.65-3.70.308850.26412381323
3.7-3.750.297630.24812181281
3.75-3.810.254790.23812341313
3.81-3.870.268540.22712461300
3.87-3.930.296730.24612351308
3.93-40.259680.2312761344
4-4.070.239590.2212281287
4.07-4.150.282700.22112481318
4.15-4.230.231640.20912441308
4.23-4.320.232730.18912241297
4.32-4.420.219630.18512221285
4.42-4.530.229640.1812491313
4.53-4.650.184580.15512831341
4.65-4.790.228760.17712211297
4.79-4.940.234790.19812551334
4.94-5.110.197740.19312191293
5.11-5.310.192790.18512581337
5.31-5.550.279610.20612461307
5.55-5.840.282530.22512681321
5.84-6.190.227710.21412751346
6.19-6.650.25550.23212651320
6.65-7.290.243720.22612621334
7.29-8.280.278800.21712591339
8.28-10.20.27630.22212881351
10.2-200.279760.25513161392
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_repADD.param
X-RAY DIFFRACTION2lig.par
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.param

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