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Yorodumi- PDB-3vjk: Crystal structure of human depiptidyl peptidase IV (DPP-4) in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vjk | |||||||||
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Title | Crystal structure of human depiptidyl peptidase IV (DPP-4) in complex with MP-513 | |||||||||
Components | Dipeptidyl peptidase 4 | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / ALPHA/BETA / BETA-PROPELLER / AMINOPEPTIDASE / SERINE PROTEASE / SIGNAL-ANCHOR / TRANSMEMBRANE / DIABETES / GLYCOPROTEIN / CELL MEMBRANE / 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 / psychomotor behavior / dipeptidyl-peptidase IV / intercellular canaliculus / 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 / 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) / lamellipodium / virus receptor activity / protease binding / receptor-mediated endocytosis of virus by host cell / membrane fusion / receptor-mediated virion attachment to host cell / cell adhesion / response to hypoxia / symbiont entry into host cell / membrane raft / apical plasma membrane / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / signaling receptor binding / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | |||||||||
Authors | Akahoshi, F. / Kishida, H. / Miyaguchi, I. / Yoshida, T. / Ishii, S. | |||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2012 Title: Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long- ...Title: Discovery and preclinical profile of teneligliptin (3-[(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-ylcarbonyl]thiazolidine): A highly potent, selective, long-lasting and orally active dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes Authors: Yoshida, T. / Akahoshi, F. / Sakashita, H. / Kitajima, H. / Nakamura, M. / Sonda, S. / Takeuchi, M. / Tanaka, Y. / Ueda, N. / Sekiguchi, S. / Ishige, T. / Shima, K. / Nabeno, M. / Abe, Y. / ...Authors: Yoshida, T. / Akahoshi, F. / Sakashita, H. / Kitajima, H. / Nakamura, M. / Sonda, S. / Takeuchi, M. / Tanaka, Y. / Ueda, N. / Sekiguchi, S. / Ishige, T. / Shima, K. / Nabeno, M. / Abe, Y. / Anabuki, J. / Soejima, A. / Yoshida, K. / Takashina, Y. / Ishii, S. / Kiuchi, S. / Fukuda, S. / Tsutsumiuchi, R. / Kosaka, K. / Murozono, T. / Nakamaru, Y. / Utsumi, H. / Masutomi, N. / Kishida, H. / Miyaguchi, I. / Hayashi, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vjk.cif.gz | 316.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vjk.ent.gz | 256 KB | Display | PDB format |
PDBx/mmJSON format | 3vjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vjk_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 3vjk_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 3vjk_validation.xml.gz | 56.7 KB | Display | |
Data in CIF | 3vjk_validation.cif.gz | 79.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/3vjk ftp://data.pdbj.org/pub/pdb/validation_reports/vj/3vjk | HTTPS FTP |
-Related structure data
Related structure data | 3vjlC 1j2eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 85880.031 Da / Num. of mol.: 2 / Fragment: UNP residues 33-766 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP4, ADCP2, CD26 / Plasmid: pPSC8 / Cell line (production host): expresSF+ / 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 Source method: isolated from a genetically manipulated source #3: Chemical | #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 20% PEG 4000, 0.18M sodium acetate, 0.18M glycine-sodium hydroxide , pH 8.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.49→50 Å / Num. all: 72839 / Num. obs: 65671 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.49→2.58 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.491 / Num. unique all: 6849 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J2E Resolution: 2.49→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.424 / SU ML: 0.213 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.503 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.554 Å / Total num. of bins used: 20
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