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- PDB-3g0d: Crystal structure of dipeptidyl peptidase IV in complex with a py... -

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Basic information

Entry
Database: PDB / ID: 3g0d
TitleCrystal structure of dipeptidyl peptidase IV in complex with a pyrimidinedione inhibitor 2
ComponentsDipeptidyl peptidase 4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DPP4 / pyrimidinone / pyrimidindione / Aminopeptidase / Cell membrane / Glycoprotein / Hydrolase / Membrane / Protease / Secreted / Serine protease / Signal-anchor / Transmembrane / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity ...glucagon processing / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / intercellular canaliculus / psychomotor behavior / chemorepellent activity / dipeptidyl-peptidase activity / peptide hormone processing / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / membrane fusion / receptor-mediated endocytosis of virus by host cell / receptor-mediated virion attachment to host cell / response to hypoxia / cell adhesion / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / signaling receptor binding / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / identical protein binding / membrane / 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 ...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-XIH / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsZhang, Z. / Wallace, M.B. / Feng, J. / Stafford, J.A. / Kaldor, S.W. / Shi, L. / Skene, R.J. / Aertgeerts, K. / Lee, B. / Jennings, A. ...Zhang, Z. / Wallace, M.B. / Feng, J. / Stafford, J.A. / Kaldor, S.W. / Shi, L. / Skene, R.J. / Aertgeerts, K. / Lee, B. / Jennings, A. / Xu, R. / Kassel, D. / Webb, D.R. / Gwaltney, S.L.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Design and Synthesis of Pyrimidinone and Pyrimidinedione Inhibitors of Dipeptidyl Peptidase IV.
Authors: Zhang, Z. / Wallace, M.B. / Feng, J. / Stafford, J.A. / Skene, R.J. / Shi, L. / Lee, B. / Aertgeerts, K. / Jennings, A. / Xu, R. / Kassel, D.B. / Kaldor, S.W. / Navre, M. / Webb, D.R. / Gwaltney, S.L.
History
DepositionJan 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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
Revision 2.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)349,89627
Polymers343,1044
Non-polymers6,79323
Water23,9061327
1
A: Dipeptidyl peptidase 4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,38215
Polymers171,5522
Non-polymers3,83013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-16.9 kcal/mol
Surface area58570 Å2
MethodPISA
2
C: Dipeptidyl peptidase 4
hetero molecules

D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,51512
Polymers171,5522
Non-polymers2,96310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y+1/2,-z1
Buried area4440 Å2
ΔGint-15.9 kcal/mol
Surface area58520 Å2
MethodPISA
3
A: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9038
Polymers85,7761
Non-polymers2,1277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4797
Polymers85,7761
Non-polymers1,7036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
C: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4797
Polymers85,7761
Non-polymers1,7036
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
D: Dipeptidyl peptidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0365
Polymers85,7761
Non-polymers1,2604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)122.905, 123.442, 145.684
Angle α, β, γ (deg.)90.000, 114.690, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Dipeptidyl peptidase 4 membrane form / Dipeptidyl peptidase IV membrane form / Dipeptidyl peptidase 4 soluble form / Dipeptidyl peptidase IV soluble form


Mass: 85775.945 Da / Num. of mol.: 4 / Fragment: UNP residues 39-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADCP2, CD26, DPP4 / Plasmid: pSXB9 / 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: isolated from a genetically manipulated source
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-XIH / 2-({8-[(3R)-3-AMINOPIPERIDIN-1-YL]-1,3-DIMETHYL-2,6-DIOXO-1,2,3,6-TETRAHYDRO-7H-PURIN-7-YL}METHYL)BENZONITRILE


Mass: 393.442 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23N7O2
#4: 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.: 14
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1327 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: 22.5% PEG MME 200, 0.1M Bicine pH 7.8, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 147841 / % possible obs: 95.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.076 / Χ2: 0.999 / Net I/σ(I): 15.284
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.39-2.462.60.52571460.99969.6
2.46-2.5230.50281321.00978.7
2.52-2.593.30.47990180.99588
2.59-2.663.50.41998951.00296.1
2.66-2.753.80.349101870.99499.1
2.75-2.853.90.289102780.997100
2.85-2.9640.212103090.992100
2.96-3.0940.163103071.004100
3.09-3.2640.113103110.983100
3.26-3.4640.085102941.007100
3.46-3.7340.068103601.001100
3.73-4.13.90.061103201.00499.9
4.1-4.73.90.05103501.012100
4.7-5.923.80.041103830.988100
5.92-5040.032105510.99599.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3G0B

3g0b


Resolution: 2.39→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.822 / SU B: 15.206 / SU ML: 0.188 / SU R Cruickshank DPI: 0.392 / SU Rfree: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.378 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 7412 5 %RANDOM
Rwork0.187 ---
obs0.189 147788 95.17 %-
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 max: 118.71 Å2 / Biso mean: 53.154 Å2 / Biso min: 25.04 Å2
Baniso -1Baniso -2Baniso -3
1--3 Å20 Å2-0.21 Å2
2--3.4 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23714 0 452 1327 25493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02224943
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.95133968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.02352888
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92223.931224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.388153971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.45915119
X-RAY DIFFRACTIONr_chiral_restr0.0840.23613
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219104
X-RAY DIFFRACTIONr_nbd_refined0.1850.210740
X-RAY DIFFRACTIONr_nbtor_refined0.3070.216783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.21420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.237
X-RAY DIFFRACTIONr_mcbond_it1.012214825
X-RAY DIFFRACTIONr_mcangle_it1.635323416
X-RAY DIFFRACTIONr_scbond_it0.971212043
X-RAY DIFFRACTIONr_scangle_it1.495310552
LS refinement shellResolution: 2.39→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 394 -
Rwork0.266 7340 -
all-7734 -
obs--67.58 %

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