[English] 日本語
Yorodumi- PDB-4uqh: Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uqh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Trypanosoma cruzi CYP51 bound to the inhibitor (R)-N-(3-(1H-indol-3-yl)-1-oxo-1-(pyridin-4-ylamino)propan-2-yl)-4-(4-(3,4-difluorophenyl)piperazin-1-yl)-2-fluorobenzamide. | ||||||
Components | STEROL 14-ALPHA DEMETHYLASE | ||||||
Keywords | OXIDOREDUCTASE / STEROL BIOSYNTHESIS / CHAGAS DISEASE | ||||||
Function / homology | Function and homology information sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / iron ion binding / heme binding / membrane Similarity search - Function | ||||||
Biological species | TRYPANOSOMA CRUZI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Calvet, C.M. / Vieira, D.F. / Choi, J.Y. / Cameron, M.D. / Gut, J. / Kellar, D. / Siqueira-Neto, J.L. / McKerrow, J.H. / Roush, W.R. / Podust, L.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: 4-Aminopyridyl-Based Cyp51 Inhibitors as Anti-Trypanosoma Cruzi Drug Leads with Improved Pharmacokinetic Profile and in Vivo Potency. Authors: Calvet, C.M. / Vieira, D.F. / Choi, J.Y. / Kellar, D. / Cameron, M.D. / Siqueira-Neto, J.L. / Gut, J. / Johnston, J.B. / Lin, L. / Khan, S. / Mckerrow, J.H. / Roush, W.R. / Podust, L.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4uqh.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4uqh.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 4uqh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqh ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqh | HTTPS FTP |
---|
-Related structure data
Related structure data | 4bmmC 4c0cSC C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 53286.820 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-481 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: Q5I4E1, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-HEM / | ||||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-25S / ( | #5: Water | ChemComp-HOH / | Nonpolymer details | PROTOPORPH | Sequence details | FIRST 32 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGKL SEQUENCE, 6XHIS TAG ...FIRST 32 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGK | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.14 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 Details: 0.3 M AMMONIUM SULFATE, 0.1 M BIS- TRIS, PH 5.5; 19% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 26, 2014 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→116.57 Å / Num. obs: 21961 / % possible obs: 100 % / Observed criterion σ(I): 0.5 / Redundancy: 12.8 % / Biso Wilson estimate: 58.7 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.43→2.56 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.99 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4C0C Resolution: 2.43→111.19 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.464 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 251-257 ARE DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.233 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→111.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|