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Yorodumi- PDB-4ajj: rat LDHA in complex with 2-((3,4-dimethoxyphenyl)methyl))propaned... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ajj | ||||||
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Title | rat LDHA in complex with 2-((3,4-dimethoxyphenyl)methyl))propanedioic acid and N-(2-methyl-1,3-benzothiazol-6-yl)-3-ureido-propanamide | ||||||
Components | L-LACTATE DEHYDROGENASE A CHAIN | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / OXIDOREDUCTASE-INHIBITOR COMPLEX / FRAGMENT BASED LEAD GENERATED INHIBITORS | ||||||
Function / homology | Function and homology information 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 ...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 / positive regulation of apoptotic process / response to xenobiotic stimulus / mitochondrion / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Tucker, J.A. / Brassington, C. / Hassall, G. / Vogtherr, M. / Ward, R. / Tart, J. / Davies, G. / Patel, J. / Greenwood, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ajj.cif.gz | 524.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ajj.ent.gz | 434.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ajj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ajj_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4ajj_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4ajj_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 4ajj_validation.cif.gz | 86.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/4ajj ftp://data.pdbj.org/pub/pdb/validation_reports/aj/4ajj | HTTPS FTP |
-Related structure data
Related structure data | 4aj1C 4aj2C 4aj4C 4ajeC 4ajhC 4ajiC 4ajkC 4ajlC 4ajnC 4ajoC 4ajpC 4al4C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) RATTUS NORVEGICUS (Norway rat) / Tissue: MUSCLE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P04642, L-lactate dehydrogenase |
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-Non-polymers , 6 types, 1156 molecules
#2: Chemical | ChemComp-88S / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-DMS / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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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: 47 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 1.5M SODIUM MALONATE PH 7.0, 2% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 17, 2010 / 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: 1.75→128.27 Å / Num. obs: 99037 / % possible obs: 76.5 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 19.98 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7 / % possible all: 14.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INTERNAL RAT LDHA STRUCTURE Resolution: 1.75→25.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.9482 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.134 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.113 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. DISORDERED SIDE-CHAINS HAVE BEEN TRUNCATED
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Displacement parameters | Biso mean: 22.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.183 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→25.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.79 Å / Total num. of bins used: 20
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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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