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- PDB-3opm: Crystal Structure of Human DPP4 Bound to TAK-294 -

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Basic information

Entry
Database: PDB / ID: 3opm
TitleCrystal Structure of Human DPP4 Bound to TAK-294
ComponentsDipeptidyl peptidase 4Dipeptidyl peptidase-4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protease and 8-bladed beta-propeller domain / Aminopeptidase / Cell membrane / Glycoprotein / Hydrolase / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane / SIGNALING PROTEIN / HYDROLASE-HYDROLASE INHIBITOR / 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 / 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-LUI / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å
AuthorsYano, J.K. / Aertgeerts, K.
CitationJournal: Bioorg.Med.Chem. / Year: 2011
Title: Identification of 3-aminomethyl-1,2-dihydro-4-phenyl-1-isoquinolones: a new class of potent, selective, and orally active non-peptide dipeptidyl peptidase IV inhibitors that form a unique interaction with Lys554.
Authors: Banno, Y. / Miyamoto, Y. / Sasaki, M. / Oi, S. / Asakawa, T. / Kataoka, O. / Takeuchi, K. / Suzuki, N. / Ikedo, K. / Kosaka, T. / Tsubotani, S. / Tani, A. / Funami, M. / Tawada, M. / ...Authors: Banno, Y. / Miyamoto, Y. / Sasaki, M. / Oi, S. / Asakawa, T. / Kataoka, O. / Takeuchi, K. / Suzuki, N. / Ikedo, K. / Kosaka, T. / Tsubotani, S. / Tani, A. / Funami, M. / Tawada, M. / Yamamoto, Y. / Aertgeerts, K. / Yano, J. / Maezaki, H.
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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

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)348,36424
Polymers343,1044
Non-polymers5,26020
Water9,116506
1
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules

C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,36424
Polymers343,1044
Non-polymers5,26020
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area14860 Å2
ΔGint40 kcal/mol
Surface area117390 Å2
MethodPISA
2
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,74415
Polymers171,5522
Non-polymers3,19213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint27 kcal/mol
Surface area58760 Å2
MethodPISA
3
C: Dipeptidyl peptidase 4
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,6209
Polymers171,5522
Non-polymers2,0687
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6790 Å2
ΔGint14 kcal/mol
Surface area59050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.771, 122.557, 144.737
Angle α, β, γ (deg.)90.00, 115.00, 90.00
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 / ADCP-2 / ADABP


Mass: 85775.945 Da / Num. of mol.: 4 / Fragment: DPP4 / Mutation: N-terminal His tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCP2, CD26, DPP4 / Plasmid: pFASTBAC / 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.: 1 / 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: Chemical
ChemComp-LUI / 2-{[3-(aminomethyl)-2-(2-methylpropyl)-1-oxo-4-phenyl-1,2-dihydroisoquinolin-6-yl]oxy}acetamide / TAK-285


Mass: 379.452 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H25N3O3
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15 / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 56.89 %
Crystal growTemperature: 277 K
Details: 23.6% PEG MME 2000, 100 mM Bicine, VAPOR DIFFUSION, SITTING DROP, temperature 277K
PH range: 8-8.5

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Data collection

DiffractionMean temperature: 92 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2007
RadiationMonochromator: SI (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.72→50 Å / Num. obs: 100745 / % possible obs: 97.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 8
Reflection shellResolution: 2.72→2.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.59 / % possible all: 82.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.91 Å48.23 Å
Translation2.91 Å48.23 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 28.408 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25447 5038 5 %RANDOM
Rwork0.19456 ---
obs0.19749 95647 97.5 %-
all-103161 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.799 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å2-0.15 Å2
2---0.12 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.72→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23857 0 350 506 24713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02224927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216594
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.94433920
X-RAY DIFFRACTIONr_angle_other_deg0.844340110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.64752907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88923.9551234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.362153984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.47615119
X-RAY DIFFRACTIONr_chiral_restr0.0710.23588
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0227646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025443
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.21018
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0550.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2060.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2921.514503
X-RAY DIFFRACTIONr_mcbond_other0.0531.55872
X-RAY DIFFRACTIONr_mcangle_it0.556223528
X-RAY DIFFRACTIONr_scbond_it0.847310424
X-RAY DIFFRACTIONr_scangle_it1.3744.510392
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.722→2.792 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 311 -
Rwork0.318 6015 -
obs--83.72 %
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)
12.20880.21510.49270.5909-0.20821.5177-0.0288-0.49490.37830.3017-0.00310.2982-0.092-0.46820.03190.19550.04370.10520.4517-0.090.22344.701-34.73428.661
22.30390.28230.39271.00010.07721.4754-0.10740.22860.3463-0.19310.08510.0856-0.004-0.08450.02220.04560.0102-0.02870.2070.02980.073222.294-30.0073.235
32.35710.47650.13750.6788-0.56431.0716-0.1121-0.2473-0.1337-0.10060.0563-0.30690.30820.20650.05580.17370.1137-0.07340.4174-0.15410.26274.363-32.91226.96
42.07090.2665-0.1821.23920.04631.2526-0.1051-0.01130.6605-0.07330.0995-0.0237-0.22860.06260.00560.05590.0071-0.0480.1731-0.05440.310555.371-12.68512.618
52.59160.6959-0.26641.65430.4350.9510.1872-0.51480.52460.24-0.38420.8512-0.1492-0.6330.1970.3225-0.05010.18250.7758-0.31080.5006-34.97538.80352.75
62.86810.9631-0.07011.75720.16741.1750.2415-0.1891-0.54890.1808-0.23380.20440.3471-0.2682-0.00770.221-0.0903-0.00030.2308-0.01540.2767-20.96214.25739.561
73.3888-0.0719-0.86210.42320.49111.36490.0649-0.7191-0.19890.22760.0297-0.19820.18870.6189-0.09470.2172-0.0011-0.09690.61860.01840.169133.8132.24940.905
82.82710.1676-0.2990.7690.17931.48830.09360.4561-0.4255-0.1236-0.0774-0.01780.20410.1282-0.01630.12320.0941-0.03080.2563-0.1040.078910.9324.920.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A61 - 495
2X-RAY DIFFRACTION2A497 - 766
3X-RAY DIFFRACTION2A1
4X-RAY DIFFRACTION3B61 - 495
5X-RAY DIFFRACTION4B497 - 766
6X-RAY DIFFRACTION4B1
7X-RAY DIFFRACTION5C61 - 495
8X-RAY DIFFRACTION6C497 - 766
9X-RAY DIFFRACTION6C1
10X-RAY DIFFRACTION7D61 - 495
11X-RAY DIFFRACTION8D497 - 766
12X-RAY DIFFRACTION8D1

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