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- PDB-2oqv: Human Dipeptidyl Peptidase IV (DPP4) with piperidine-constrained ... -

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Basic information

Entry
Database: PDB / ID: 2oqv
TitleHuman Dipeptidyl Peptidase IV (DPP4) with piperidine-constrained phenethylamine
ComponentsDipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
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 / 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-MA9 / 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.
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
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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)
B: Dipeptidyl peptidase 4 (Dipeptidyl peptidase IV) (DPP IV)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,9673
Polymers168,5052
Non-polymers4621
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-14 kcal/mol
Surface area57990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.012, 118.203, 232.517
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 2 / Auth seq-ID: 39 - 764 / Label seq-ID: 1 - 726

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe dimer of the asymmetric unit is thought to be biologically relevant.

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Components

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


Mass: 84252.336 Da / Num. of mol.: 2
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-MA9 / (3R,4R)-1-{6-[3-(METHYLSULFONYL)PHENYL]PYRIMIDIN-4-YL}-4-(2,4,5-TRIFLUOROPHENYL)PIPERIDIN-3-AMINE


Mass: 462.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21F3N4O2S

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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: 2.65 Å3/Da / Density % sol: 53.59 %
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-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / 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: 37666 / % possible obs: 82.2 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.21 / Χ2: 1.483 / Net I/σ(I): 4.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.95.50.64737150.68782.4
2.9-3.025.50.55737360.82783
3.02-3.155.50.47237310.97882.3
3.15-3.325.50.39237211.18682.7
3.32-3.535.40.36436911.73281.7
3.53-3.85.40.27136951.92581
3.8-4.185.30.20836552.18380.1
4.18-4.795.30.12936932.0180.3
4.79-6.035.20.10637251.51780
6.03-505.20.08543041.86388.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→119.52 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.841 / SU B: 18.334 / SU ML: 0.364 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.547 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1884 5.1 %RANDOM
Rwork0.243 ---
obs0.246 37014 82.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.281 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20 Å2
2--1.25 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→119.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11898 0 32 0 11930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212285
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.93216718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.96451450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50623.961616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.086151990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5211560
X-RAY DIFFRACTIONr_chiral_restr0.1120.21755
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029520
X-RAY DIFFRACTIONr_nbd_refined0.2260.25677
X-RAY DIFFRACTIONr_nbtor_refined0.3190.28304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2377
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.23
X-RAY DIFFRACTIONr_mcbond_it0.4281.57394
X-RAY DIFFRACTIONr_mcangle_it0.778211741
X-RAY DIFFRACTIONr_scbond_it1.135765
X-RAY DIFFRACTIONr_scangle_it1.7534.54977
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2904TIGHT POSITIONAL0.060.05
3045MEDIUM POSITIONAL0.360.5
2904TIGHT THERMAL0.080.5
3045MEDIUM THERMAL0.542
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.427 142 -
Rwork0.318 2495 -
obs-2637 82.64 %

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