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- PDB-4aj1: rat LDHA in complex with N-(2-(methylamino)-1,3-benzothiazol-6-yl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aj1 | ||||||
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Title | rat LDHA in complex with N-(2-(methylamino)-1,3-benzothiazol-6-yl) acetamide | ||||||
![]() | L-LACTATE DEHYDROGENASE A CHAIN | ||||||
![]() | OXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR COMPLEX / FRAGMENT BASED LEAD GENERATED INHIBITORS | ||||||
Function / homology | ![]() lactate dehydrogenase activity / Pyruvate metabolism / Regulation of pyruvate metabolism / sperm fibrous sheath / pyruvate catabolic process / oxidoreductase complex / : / L-lactate dehydrogenase / NAD metabolic process / lactate metabolic process ...lactate dehydrogenase activity / Pyruvate metabolism / Regulation of pyruvate metabolism / sperm fibrous sheath / pyruvate catabolic process / oxidoreductase complex / : / L-lactate dehydrogenase / NAD metabolic process / lactate metabolic process / L-lactate dehydrogenase activity / glucose catabolic process to lactate via pyruvate / pyruvate metabolic process / response to glucose / skeletal muscle tissue development / response to cAMP / response to nutrient / liver development / response to hydrogen peroxide / response to organic cyclic compound / kinase binding / response to estrogen / NAD binding / response to hypoxia / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tucker, J.A. / Brassington, C. / Hassall, G. / Vogtherr, M. / Ward, R. / Tart, J. / Davies, G. | ||||||
![]() | ![]() Title: The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation Authors: Ward, R. / Brassington, C. / Breeze, A.L. / Caputo, A. / Critchlow, S. / Davies, G. / Goodwin, L. / Hassall, G. / Greenwood, R. / Holdgate, G. / Mrosek, M. / Norman, R.A. / Pearson, S. / ...Authors: Ward, R. / Brassington, C. / Breeze, A.L. / Caputo, A. / Critchlow, S. / Davies, G. / Goodwin, L. / Hassall, G. / Greenwood, R. / Holdgate, G. / Mrosek, M. / Norman, R.A. / Pearson, S. / Tart, J. / Tucker, J.A. / Vogtherr, M. / Whittaker, D. / Wingfield, J. / Winter, J. / Hudson, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 515.6 KB | Display | ![]() |
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PDB format | ![]() | 427.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4aj2C ![]() 4aj4C ![]() 4ajeC ![]() 4ajhC ![]() 4ajiC ![]() 4ajjC ![]() 4ajkC ![]() 4ajlC ![]() 4ajnC ![]() 4ajoC ![]() 4ajpC ![]() 4al4C 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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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 36363.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1042 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/AJ1.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AJ1.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/OXM.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-AJ1 / #4: Chemical | ChemComp-MLI / #5: Chemical | ChemComp-OXM / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.5 M NA MALONATE PH 7.0, 2% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 8, 2008 / Details: VARIMAXHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→64.06 Å / Num. obs: 78548 / % possible obs: 73.8 % / Observed criterion σ(I): 2 / Redundancy: 2.81 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.87→1.94 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.2 / % possible all: 33.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: INTERNAL RAT LDHA STRUCTURE Resolution: 1.87→49.37 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.652 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.232 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. DISORDERED SIDE-CHAINS HAVE BEEN TRUNCATED
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.782 Å2
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Refinement step | Cycle: LAST / Resolution: 1.87→49.37 Å
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Refine LS restraints |
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