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- PDB-2ci0: High throughput screening and x-ray crystallography assisted eval... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ci0 | ||||||
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Title | High throughput screening and x-ray crystallography assisted evaluation of small molecule scaffolds for CYP51 inhibitors | ||||||
![]() | CYTOCHROME P450 51 | ||||||
![]() | OXIDOREDUCTASE / HEME / HEME LIPID SYNTHESIS / METAL-BINDING / MONOOXYGENASE / NADP / PROTEIN-INHIBITOR COMPLEX / STEROID BIOSYNTHESIS / STEROL BIOSYNTHESIS | ||||||
Function / homology | ![]() sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol biosynthetic process / sterol metabolic process / bile acid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity ...sterol 14alpha-demethylase (ferredoxin) / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol biosynthetic process / sterol metabolic process / bile acid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / cholesterol homeostasis / oxidoreductase activity / iron ion binding / heme binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Podust, L.M. / Kim, Y. / Yermalitskaya, L.V. / Von Kries, J.P. / Waterman, M.R. | ||||||
![]() | ![]() Title: Small Molecule Scaffolds for Cyp51 Inhibitors Identified by High Throughput Screening and Defined by X-Ray Crystallography Authors: Podust, L.M. / Von Kries, J.P. / Eddine, A.N. / Kim, Y. / Yermalitskaya, L.V. / Kuehne, R. / Ouellet, H. / Warrier, T. / Altekoster, M. / Lee, J.-S. / Rademann, J. / Oschkinat, H. / ...Authors: Podust, L.M. / Von Kries, J.P. / Eddine, A.N. / Kim, Y. / Yermalitskaya, L.V. / Kuehne, R. / Ouellet, H. / Warrier, T. / Altekoster, M. / Lee, J.-S. / Rademann, J. / Oschkinat, H. / Kaufmann, S.H.E. / Waterman, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.2 KB | Display | ![]() |
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PDB format | ![]() | 82.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 31.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bz9C ![]() 2cibC ![]() 1x8vS S: Starting model for refinement 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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Components
#1: Protein | Mass: 51477.285 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: 4XHIS TAG AT THE C-TERMINUS / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A512, UniProt: P9WPP9*PLUS, sterol 14alpha-demethylase | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-1CM / ( | ||
#4: Water | ChemComp-HOH / | ||
Compound details | ENGINEEREDSequence details | MUTATIONS C37L, C442A 4XHIS TAG AT THE C-TERMINUS | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 40 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 15 % PEG 4000,1% ISOPROPANOL, 0.1 M HEPES, PH=7.5; 2 MM (2R)-2-PHENYL-N-PYRIDIN-4- YLBUTANAMIDE |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 3, 2006 Details: SAGITTAL FOCUSING CRYSTAL AND VERTICALLY FOCUSING DOUBLE MIRROR |
Radiation | Monochromator: SI (220) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00931 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 65111 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 47.7 |
Reflection shell | Resolution: 1.53→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9 / % possible all: 89.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1X8V Resolution: 1.53→46.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 322653.73 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: DISORDERED REGIONS DISORDERED REGIONS WERE OMMITED FROM THE STRUCTURE
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3122 Å2 / ksol: 0.38274 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.53→46.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.63 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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