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- PDB-8hb9: Crystal Structure of Human IDH1 R132H Mutant in Complex with NADP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hb9 | |||||||||||||||||||||
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Title | Crystal Structure of Human IDH1 R132H Mutant in Complex with NADPH and Compound IHMT-IDH1-053 | |||||||||||||||||||||
![]() | Isocitrate dehydrogenase [NADP] cytoplasmic | |||||||||||||||||||||
![]() | OXIDOREDUCTASE | |||||||||||||||||||||
Function / homology | ![]() Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / tertiary granule lumen / peroxisome / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||
Method | ![]() ![]() | |||||||||||||||||||||
![]() | Guo, G. / Wang, B. / Liu, J. / Liu, Q. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-based discovery of IHMT-IDH1-053 as a potent irreversible IDH1 mutant selective inhibitor. Authors: Liang, Q. / Wang, B. / Zou, F. / Guo, G. / Wang, W. / Wang, W. / Liu, Q. / Shen, L. / Hu, C. / Wang, W. / Wang, A. / Huang, T. / He, Y. / Xia, R. / Ge, J. / Liu, J. / Liu, Q. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 345.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6b0zS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: 1
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 46701.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75874, isocitrate dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 272 molecules ![](data/chem/img/R1R.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NDP.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-R1R / [ #3: Chemical | ChemComp-NDP / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.67 % |
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Crystal grow | Temperature: 315 K / Method: vapor diffusion, sitting drop / Details: 24% PEG 3350, 8% Tacsimate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→13.078 Å / Num. obs: 53443 / % possible obs: 99 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.8→2.89 Å / Rmerge(I) obs: 0.606 / Num. unique obs: 4636 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6b0z Resolution: 2.8→13.078 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.895 / SU B: 16.165 / SU ML: 0.292 / Cross valid method: FREE R-VALUE / ESU R Free: 0.357 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.89 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→13.078 Å
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Refine LS restraints |
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