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Yorodumi- PDB-7vbv: Crystal structure of human pyruvate dehydrogenase kinase 2 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7vbv | ||||||
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Title | Crystal structure of human pyruvate dehydrogenase kinase 2 in complex with compound 7 | ||||||
Components | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | ||||||
Keywords | TRANSFERASE/INHIBITOR / PDHK / KINASE INHIBITORS / FRAGMENT SCREENING / PDK1 / PDK2 / PDK3 / PDK4 / TRANSFERASE-INHIBITOR complex | ||||||
Function / homology | Function and homology information [pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / : / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / regulation of gluconeogenesis ...[pyruvate dehydrogenase (acetyl-transferring)] kinase / regulation of acetyl-CoA biosynthetic process from pyruvate / pyruvate dehydrogenase (acetyl-transferring) kinase activity / : / regulation of cellular ketone metabolic process / regulation of pH / cellular response to nutrient / Regulation of pyruvate dehydrogenase (PDH) complex / Signaling by Retinoic Acid / regulation of gluconeogenesis / intrinsic apoptotic signaling pathway by p53 class mediator / regulation of glucose metabolic process / regulation of calcium-mediated signaling / cellular response to reactive oxygen species / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / mitochondrial matrix / protein kinase activity / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Orita, T. / Doi, S. / Iwanaga, T. / Fujishima, A. / Adachi, T. | ||||||
Funding support | 1items
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Citation | Journal: Bioorg.Med.Chem. / Year: 2021 Title: Structure-based drug design of novel and highly potent pyruvate dehydrogenase kinase inhibitors. Authors: Bessho, Y. / Akaki, T. / Hara, Y. / Yamakawa, M. / Obika, S. / Mori, G. / Ubukata, M. / Yasue, K. / Nakane, Y. / Terasako, Y. / Orita, T. / Doi, S. / Iwanaga, T. / Fujishima, A. / Adachi, T. ...Authors: Bessho, Y. / Akaki, T. / Hara, Y. / Yamakawa, M. / Obika, S. / Mori, G. / Ubukata, M. / Yasue, K. / Nakane, Y. / Terasako, Y. / Orita, T. / Doi, S. / Iwanaga, T. / Fujishima, A. / Adachi, T. / Ueno, H. / Motomura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vbv.cif.gz | 323.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vbv.ent.gz | 235.2 KB | Display | PDB format |
PDBx/mmJSON format | 7vbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vb/7vbv ftp://data.pdbj.org/pub/pdb/validation_reports/vb/7vbv | HTTPS FTP |
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-Related structure data
Related structure data | 7vbuC 7vbxC 7ebhS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 44647.730 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PDK2, PDHK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q15119, [pyruvate dehydrogenase (acetyl-transferring)] kinase |
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-Non-polymers , 5 types, 94 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.26 Å3/Da / Density % sol: 62.22 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 50 mM Na acetate pH 5.5, 100 mM magnesium chloride and 8% (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 23, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→94.66 Å / Num. obs: 54702 / % possible obs: 97.3 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.031 / Rrim(I) all: 0.073 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.21→2.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4081 / CC1/2: 0.839 / Rpim(I) all: 0.311 / Rrim(I) all: 0.724 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EBH Resolution: 2.21→62.95 Å / Cross valid method: FREE R-VALUE / σ(F): 55.14 / Phase error: 26.9241 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→62.95 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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