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- PDB-3ccb: Crystal Structure of Human DPP4 in complex with a benzimidazole d... -

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Basic information

Entry
Database: PDB / ID: 3ccb
TitleCrystal Structure of Human DPP4 in complex with a benzimidazole derivative
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE / structure-based design / denzimidazole derivatives / peptidase / Aminopeptidase / Glycoprotein / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane
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 / 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 / dipeptidyl-peptidase IV / psychomotor behavior / 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 / 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
1-biphenyl-2-ylmethanamine / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.49 Å
AuthorsWallace, M.B. / Skene, R.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Structure-based design and synthesis of benzimidazole derivatives as dipeptidyl peptidase IV inhibitors.
Authors: Wallace, M.B. / Feng, J. / Zhang, Z. / Skene, R.J. / Shi, L. / Caster, C.L. / Kassel, D.B. / Xu, R. / Gwaltney, S.L.
History
DepositionFeb 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)348,61325
Polymers343,1044
Non-polymers5,50921
Water12,178676
1
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,96115
Polymers171,5522
Non-polymers3,40913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint30.3 kcal/mol
Surface area59110 Å2
MethodPISA
2
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,65210
Polymers171,5522
Non-polymers2,1008
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint13 kcal/mol
Surface area58410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.086, 123.010, 144.651
Angle α, β, γ (deg.)90.000, 114.840, 90.000
Int Tables number4
Space group name H-MP1211

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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: 85775.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 5 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / 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
#4: Chemical
ChemComp-B2Y / 1-biphenyl-2-ylmethanamine


Mass: 183.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H13N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 22.5% PEG 2000mme, 0.1M Bicine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Aug 8, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 133909 / % possible obs: 98.9 % / Rmerge(I) obs: 0.068 / Χ2: 1.072 / Net I/σ(I): 11.2
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.590.531133340.979199.4
2.59-2.690.388134921.078199.6
2.69-2.820.284134131.017199.8
2.82-2.960.19135151.017199.7
2.96-3.150.125134151.064199.6
3.15-3.390.083134491.152199.5
3.39-3.730.061134271.26199.1
3.73-4.270.046133781.091198.7
4.27-5.380.037133541.008198.2
5.38-500.031131321.045195.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 2.49→32.8 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.781 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.244 6730 5 %RANDOM
Rwork0.2 ---
obs0.202 133885 98.26 %-
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: 50.879 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å20 Å21.05 Å2
2--2.13 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.49→32.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23752 0 364 676 24792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02224876
X-RAY DIFFRACTIONr_angle_refined_deg1.2391.94633856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.34452896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96423.9381224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.156153969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.02615118
X-RAY DIFFRACTIONr_chiral_restr0.0880.23602
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219082
X-RAY DIFFRACTIONr_nbd_refined0.1970.211711
X-RAY DIFFRACTIONr_nbtor_refined0.3120.216940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.21263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.235
X-RAY DIFFRACTIONr_mcbond_it1.025214778
X-RAY DIFFRACTIONr_mcangle_it1.648323455
X-RAY DIFFRACTIONr_scbond_it0.962211811
X-RAY DIFFRACTIONr_scangle_it1.459310401
LS refinement shellResolution: 2.487→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 470 -
Rwork0.296 8663 -
all-9133 -
obs--90.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19380.2398-0.00870.74490.02740.8055-0.068-0.1708-0.25290.11380.0498-0.22980.00630.21780.0182-0.1330.0645-0.0085-0.16880.0461-0.133249.711-0.8619.105
21.5944-0.0126-0.25970.75270.15110.6754-0.1276-0.1466-0.2463-0.01480.08410.2237-0.0382-0.15840.0435-0.13070.04740.0332-0.1660.1193-0.1033-6.222-7.34320.997
31.97480.02670.39720.55660.14110.72040.10310.2450.1922-0.0608-0.0305-0.1567-0.08670.3577-0.0726-0.0783-0.060.0259-0.0835-0.0152-0.1785-36.059-0.5-33.366
41.2573-0.00640.11870.9001-0.3060.85520.0681-0.21330.07150.0834-0.1636-0.4139-0.00170.40760.0955-0.0282-0.0363-0.04620.02470.0543-0.0098-31.207-63.36946.838
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA - E41 - 80115 - 1
2X-RAY DIFFRACTION2BB - K36 - 80110 - 1
3X-RAY DIFFRACTION3CC - P41 - 80115 - 1
4X-RAY DIFFRACTION4DD - S41 - 80115 - 1

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