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Yorodumi- PDB-7ezf: Indole-2-carboxylic acid derivatives as allosteric inhibitors of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ezf | ||||||
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Title | Indole-2-carboxylic acid derivatives as allosteric inhibitors of fructose-1,6-bisphosphatase | ||||||
Components | Fructose-1,6-bisphosphatase 1 | ||||||
Keywords | HYDROLASE / fructose-1 / 6-bisphosphatase / indole dicarboxylic acid derivative inhibitor | ||||||
Function / homology | Function and homology information cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis ...cellular response to raffinose / sucrose biosynthetic process / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / cellular response to magnesium ion / negative regulation of Ras protein signal transduction / fructose 6-phosphate metabolic process / Gluconeogenesis / fructose metabolic process / monosaccharide binding / negative regulation of glycolytic process / fructose 1,6-bisphosphate metabolic process / cellular hyperosmotic salinity response / regulation of gluconeogenesis / AMP binding / dephosphorylation / cellular response to cAMP / response to nutrient levels / gluconeogenesis / negative regulation of cell growth / cellular response to insulin stimulus / cellular response to xenobiotic stimulus / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Wang, X.Y. / Zhou, J. / Xu, B.L. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2022 Title: Discovery of Novel Indole Derivatives as Fructose-1,6-bisphosphatase Inhibitors and X-ray Cocrystal Structures Analysis. Authors: Wang, X. / Zhao, R. / Ji, W. / Zhou, J. / Liu, Q. / Zhao, L. / Shen, Z. / Liu, S. / Xu, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ezf.cif.gz | 257.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ezf.ent.gz | 207.3 KB | Display | PDB format |
PDBx/mmJSON format | 7ezf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ezf_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 7ezf_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 7ezf_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 7ezf_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/7ezf ftp://data.pdbj.org/pub/pdb/validation_reports/ez/7ezf | HTTPS FTP |
-Related structure data
Related structure data | 7ezpC 7ezrC 2fieS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36887.434 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FBP1, FBP / Production host: Escherichia coli (E. coli) / References: UniProt: P09467, fructose-bisphosphatase #2: Chemical | ChemComp-0KI / #3: Sugar | ChemComp-FBP / #4: Water | ChemComp-HOH / | 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: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2M Ammonium acetate, 0.1M HEPES, 20% PEG 3350, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.76→47.78 Å / Num. obs: 33781 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Net I/σ(I): 13.6 / Num. measured all: 232384 / Scaling rejects: 82 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FIE Resolution: 2.76→47.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.905 / SU B: 14.279 / SU ML: 0.281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.04 Å2 / Biso mean: 40.721 Å2 / Biso min: 13.96 Å2
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Refinement step | Cycle: final / Resolution: 2.76→47.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.83 Å / Rfactor Rfree error: 0
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