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- PDB-4j3j: Crystal Structure of DPP-IV with Compound C3 -

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Basic information

Entry
Database: PDB / ID: 4j3j
TitleCrystal Structure of DPP-IV with Compound C3
ComponentsDipeptidyl peptidase 4
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor complex / serine exopeptidase / 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 / 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 / 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-D3C / Dipeptidyl peptidase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsXiong, B. / Zhu, L.R. / Chen, D.Q. / Zhao, Y.L. / Jiang, F. / Shen, J.K.
CitationJournal: Chemmedchem / Year: 2013
Title: Design and synthesis of 4-(2,4,5-trifluorophenyl)butane-1,3-diamines as dipeptidyl peptidase IV inhibitors
Authors: Zhu, L. / Li, Y. / Qiu, L. / Su, M. / Wang, X. / Xia, C. / Qu, Y. / Li, J. / Li, J. / Xiong, B. / Shen, J.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_initial_refinement_model / 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,7944
Polymers168,9252
Non-polymers8692
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-17 kcal/mol
Surface area59090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.648, 79.648, 292.267
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 1 / Auth seq-ID: 40 - 764 / Label seq-ID: 2 - 726

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Dipeptidyl peptidase 4 / ADABP / Adenosine deaminase complexing protein 2 / ADCP-2 / Dipeptidyl peptidase IV / DPP IV / T- ...ADABP / Adenosine deaminase complexing protein 2 / ADCP-2 / Dipeptidyl peptidase IV / DPP IV / T-cell activation antigen CD26 / TP103 / Dipeptidyl peptidase 4 soluble form / Dipeptidyl peptidase IV soluble form


Mass: 84462.617 Da / Num. of mol.: 2 / Fragment: UNP residues 39-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4 / Plasmid: pTT28 / Cell line (production host): 293F cell / Production host: Homo sapiens (human) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Chemical ChemComp-D3C / N-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butyl]-6-(trifluoromethyl)-3,4-dihydropyrrolo[1,2-a]pyrazine-2(1H)-carboxamide


Mass: 434.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20F6N4O
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: 3.17 Å3/Da / Density % sol: 61.18 % / Mosaicity: 0.837 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 28%(w/v) PEG1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. obs: 35912 / % possible obs: 99.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.069 / Χ2: 1.074 / Net I/σ(I): 9.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.15-3.265.80.70235751.0641100
3.26-3.395.90.45735871.1031100
3.39-3.555.90.31936311.0751100
3.55-3.735.90.21135771.138199.9
3.73-3.975.90.15436341.205199.9
3.97-4.275.90.09935511.163199.9
4.27-4.75.80.06536351.009199.7
4.7-5.385.80.0635661.049199.4
5.38-6.765.90.0535810.99199.8
6.76-305.70.03135750.941198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HAC

3hac


Resolution: 3.2→29.7 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / SU B: 26.563 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.535 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1695 5 %RANDOM
Rwork0.2253 ---
obs0.2274 34045 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 219.1 Å2 / Biso mean: 119.0278 Å2 / Biso min: 67.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.16 Å20 Å2
2--0.16 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11899 0 60 0 11959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0212316
X-RAY DIFFRACTIONr_angle_refined_deg0.8231.93516763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.651450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.24823.961616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.301151990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6261560
X-RAY DIFFRACTIONr_chiral_restr0.0580.21757
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219536
X-RAY DIFFRACTIONr_mcbond_it2.20111.8295806
X-RAY DIFFRACTIONr_mcangle_it3.7917.7457254
X-RAY DIFFRACTIONr_scbond_it1.98111.9326510
Refine LS restraints NCSNumber: 1148 / Type: TIGHT THERMAL / Rms dev position: 5.5 Å / Weight position: 0.5
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.439 110 -
Rwork0.361 2324 -
all-2434 -
obs--99.96 %

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