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- PDB-2iiv: Human dipeptidyl peptidase 4 in complex with a diazepan-2-one inh... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2iiv | |||||||||
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Title | Human dipeptidyl peptidase 4 in complex with a diazepan-2-one inhibitor | |||||||||
![]() | Dipeptidyl peptidase 4 soluble form | |||||||||
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Function / homology | ![]() 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 / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Scapin, G. / Weber, A.E. / Biftu, T. | |||||||||
![]() | ![]() Title: (3R)-4-[(3R)-3-Amino-4-(2,4,5-trifluorophenyl)butanoyl]-3-(2,2,2-trifluoroethyl)-1,4-diazepan-2-one, a selective dipeptidyl peptidase IV inhibitor for the treatment of type 2 diabetes Authors: Biftu, T. / Feng, D. / Qian, X. / Liang, G.B. / Kieczykowski, G. / Eiermann, G. / He, H. / Leiting, B. / Lyons, K. / Petrov, A. / Sinha-Roy, R. / Zhang, B. / Scapin, G. / Patel, S. / Gao, Y. ...Authors: Biftu, T. / Feng, D. / Qian, X. / Liang, G.B. / Kieczykowski, G. / Eiermann, G. / He, H. / Leiting, B. / Lyons, K. / Petrov, A. / Sinha-Roy, R. / Zhang, B. / Scapin, G. / Patel, S. / Gao, Y.D. / Singh, S. / Wu, J. / Zhang, X. / Thornberry, N.A. / Weber, A.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331.6 KB | Display | ![]() |
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PDB format | ![]() | 266.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2iitC ![]() 1x70S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 84476.648 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN (residues 39-766) / Mutation: Ser39Thr Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #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: Sugar | ChemComp-NAG / ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 4000, SODIUM ACETATE, TRIS, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→50 Å / Num. all: 111431 / Num. obs: 107977 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 1.2 / Num. unique all: 8273 / % possible all: 86.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1X70 Resolution: 2.15→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: MASK / Bsol: 25.8 Å2 / ksol: 0.329 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.23 Å / Total num. of bins used: 10
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