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- PDB-2jid: Human Dipeptidyl peptidase IV in complex with 1-(3,4-Dimethoxy-ph... -

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Basic information

Entry
Database: PDB / ID: 2jid
TitleHuman Dipeptidyl peptidase IV in complex with 1-(3,4-Dimethoxy-phenyl) -3-m-tolyl-piperidine-4-ylamine
ComponentsDIPEPTIDYL PEPTIDASE 4
KeywordsHYDROLASE / DIABETES TYPE II / DIPEPTIDYL PEPTIDASE / PROTEASE / MEMBRANE / B-PROPELLER / STRUCTURE BASED DESIGN / GLYCOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE / HYDROLASE FOLD / AMINOPEPTIDASE / SERINE PROTEASE
Function / homology
Function and homology information


glucagon processing / regulation of cell-cell adhesion mediated by integrin / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing ...glucagon processing / regulation of cell-cell adhesion mediated by integrin / negative regulation of neutrophil chemotaxis / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / chemorepellent activity / intercellular canaliculus / dipeptidyl-peptidase activity / peptide hormone processing / lamellipodium membrane / aminopeptidase activity / endothelial cell migration / endocytic vesicle / T cell costimulation / receptor-mediated endocytosis of virus by host cell / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / response to hypoxia / membrane fusion / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / membrane raft / serine-type endopeptidase activity / signaling receptor binding / focal adhesion / lysosomal membrane / positive regulation of cell population proliferation / symbiont entry into host cell / 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 / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / 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-GVB / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsHennig, M. / Stihle, M. / Luebbers, T. / Thoma, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: 1,3-Disubstituted 4-Aminopiperidines as Useful Tools in the Optimization of the 2-Aminobenzo[A]Quinolizine Dipeptidyl Peptidase Iv Inhibitors.
Authors: Lubbers, T. / Bohringer, M. / Gobbi, L. / Hennig, M. / Hunziker, D. / Kuhn, B. / Loffler, B. / Mattei, P. / Narquizian, R. / Peters, J. / Ruff, Y. / Wessel, H.P. / Wyss, P.
History
DepositionFeb 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,84112
Polymers170,4192
Non-polymers2,42310
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-12 kcal/mol
Surface area72620 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.251, 66.821, 423.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 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: 85209.289 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GVB / (3R,4S)-1-(3,4-DIMETHOXYPHENYL)-3-(3-METHYLPHENYL)PIPERIDIN-4-AMINE


Mass: 326.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.64 % / Description: NONE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 47000 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.819 / SU B: 18.59 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2341 5.1 %RANDOM
Rwork0.223 ---
obs0.227 43780 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2--1.12 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11926 0 160 128 12214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02212448
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.94416940
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.44451454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26823.961616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.466151994
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0071560
X-RAY DIFFRACTIONr_chiral_restr0.110.21796
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.26000
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.28305
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2466
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5931.57384
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.058211766
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.32335917
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1134.55174
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.95 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.418 350
Rwork0.287 6003

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