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Yorodumi- PDB-1boz: STRUCTURE-BASED DESIGN AND SYNTHESIS OF LIPOPHILIC 2,4-DIAMINO-6-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1boz | ||||||
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Title | STRUCTURE-BASED DESIGN AND SYNTHESIS OF LIPOPHILIC 2,4-DIAMINO-6-SUBSTITUTED QUINAZOLINES AND THEIR EVALUATION AS INHIBITORS OF DIHYDROFOLATE REDUCTASE AND POTENTIAL ANTITUMOR AGENTS | ||||||
Components | PROTEIN (DIHYDROFOLATE REDUCTASE) | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Gangjee, A. / Vidwans, A.P. / Vasudevan, A. / Queener, S.F. / Kisliuk, R.L. / Cody, V. / Li, R. / Galitsky, N. / Luft, J.R. / Pangborn, W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 1998 Title: Structure-based design and synthesis of lipophilic 2,4-diamino-6-substituted quinazolines and their evaluation as inhibitors of dihydrofolate reductases and potential antitumor agents. Authors: Gangjee, A. / Vidwans, A.P. / Vasudevan, A. / Queener, S.F. / Kisliuk, R.L. / Cody, V. / Li, R. / Galitsky, N. / Luft, J.R. / Pangborn, W. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1997 Title: Comparison of Ternary Complexes of Pneumocystis carinii and Wild-Type Human Dihydrofolate Reductase With a Novel Classical Antitumor Furo[2,3-d]pyrimidine Antifolate Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Gangjee, A. / Devraj, R. / Queener, S.F. / Blakley, R.L. #2: Journal: Biochemistry / Year: 1997 Title: Comparison of Two Independent Crystal Structures of Human Dihydrofolate Reductase Ternary Complexes Reduced with Nicotinamide Adenine Dinucleotide Phosphate and the Very Tight-Binding Inhibitor Pt523 Authors: Cody, V. / Galitsky, N. / Luft, J.R. / Pangborn, W. / Rosowsky, A. / Blakley, R.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1boz.cif.gz | 56 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1boz.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1boz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/1boz ftp://data.pdbj.org/pub/pdb/validation_reports/bo/1boz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21259.402 Da / Num. of mol.: 1 / Mutation: F31G / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00374, dihydrofolate reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-PRD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.93 % | |||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→53 Å / Num. obs: 9706 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.049 |
Reflection shell | Highest resolution: 2.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.125 / % possible all: 78 |
Reflection | *PLUS % possible obs: 86.4 % / Rmerge(I) obs: 0.0496 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 63.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 19.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / σ(F): 2 / Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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