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- PDB-6w0x: Structure of KHK in complex with compound 4 (6-[(1~{S},5~{R})-6-(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6w0x | ||||||
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Title | Structure of KHK in complex with compound 4 (6-[(1~{S},5~{R})-6-(hydroxymethyl)-3-azabicyclo[3.1.0]hexan-3-yl]-2-[(2~{S},3~{R})-2-methyl-3-oxidanyl-azetidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile) | ||||||
![]() | Ketohexokinase | ||||||
![]() | TRANSFERASE / Ketohexokinase | ||||||
Function / homology | ![]() Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose ...Essential fructosuria / ketohexokinase / ketohexokinase activity / Fructose catabolism / regulation of glycogen metabolic process / response to sucrose / response to fructose / fructose metabolic process / response to zinc ion / response to glucose / response to insulin / extracellular exosome / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jasti, J. | ||||||
![]() | ![]() Title: Discovery of PF-06835919: A Potent Inhibitor of Ketohexokinase (KHK) for the Treatment of Metabolic Disorders Driven by the Overconsumption of Fructose. Authors: Futatsugi, K. / Smith, A.C. / Tu, M. / Raymer, B. / Ahn, K. / Coffey, S.B. / Dowling, M.S. / Fernando, D.P. / Gutierrez, J.A. / Huard, K. / Jasti, J. / Kalgutkar, A.S. / Knafels, J.D. / ...Authors: Futatsugi, K. / Smith, A.C. / Tu, M. / Raymer, B. / Ahn, K. / Coffey, S.B. / Dowling, M.S. / Fernando, D.P. / Gutierrez, J.A. / Huard, K. / Jasti, J. / Kalgutkar, A.S. / Knafels, J.D. / Pandit, J. / Parris, K.D. / Perez, S. / Pfefferkorn, J.A. / Price, D.A. / Ryder, T. / Shavnya, A. / Stock, I.A. / Tsai, A.S. / Tesz, G.J. / Thuma, B.A. / Weng, Y. / Wisniewska, H.M. / Xing, G. / Zhou, J. / Magee, T.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253 KB | Display | ![]() |
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PDB format | ![]() | 202.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6w0nC ![]() 6w0wC ![]() 6w0yC ![]() 6w0zC ![]() 5wbmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34076.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 17-20% PEG8000, 100 mM sodium citrate, pH 4.4-4.7, 0.2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→70.96 Å / Num. obs: 58088 / % possible obs: 93.6 % / Redundancy: 6.5 % / CC1/2: 0.999 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 2.38→2.39 Å / Num. unique obs: 400 / CC1/2: 0.791 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5WBM Resolution: 2.38→20.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.2 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.159
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Displacement parameters | Biso max: 164.22 Å2 / Biso mean: 71.74 Å2 / Biso min: 34.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.38→20.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.38→2.48 Å / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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