+Open data
-Basic information
Entry | Database: PDB / ID: 8ug3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of KHK-C and compound 23 | ||||||
Components | Ketohexokinase | ||||||
Keywords | SUGAR BINDING PROTEIN / Inhibitor | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å | ||||||
Authors | Durbin, J.D. / Guo, S.Y. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2023 Title: Identification of LY3522348: A Highly Selective and Orally Efficacious Ketohexokinase Inhibitor. Authors: Durham, T.B. / Hao, J. / Spinazze, P. / Stack, D.R. / Toth, J.L. / Massey, S. / Mbofana, C.T. / Johnston, R.D. / Lineswala, J.P. / Wrobleski, A. / Minguez, J.M. / Perez, C. / Smith, D.L. / ...Authors: Durham, T.B. / Hao, J. / Spinazze, P. / Stack, D.R. / Toth, J.L. / Massey, S. / Mbofana, C.T. / Johnston, R.D. / Lineswala, J.P. / Wrobleski, A. / Minguez, J.M. / Perez, C. / Smith, D.L. / Lamar, J. / Leon, R. / Corkins, C. / Durbin, J. / Tung, F. / Guo, S. / Linder, R.J. / Yumibe, N. / Wang, W. / MacKrell, J. / Antonellis, M. / Mascaro, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ug3.cif.gz | 139 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ug3.ent.gz | 106.5 KB | Display | PDB format |
PDBx/mmJSON format | 8ug3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/8ug3 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/8ug3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ug1C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34276.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KHK / Production host: Escherichia coli (E. coli) / References: UniProt: P50053 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.82 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: Polyethylene glycol 8,000, Ammonium Sulfate, tri-Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→39.38 Å / Num. obs: 63482 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.02→2.13 Å / Rmerge(I) obs: 0.456 / Num. unique obs: 9158 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→39.38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.967 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.644 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.02→39.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|