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Yorodumi- PDB-8fuj: HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fuj | |||||||||
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Title | HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyrimidin-2-amine as P2-P3 group and 3,5-difluorophenylmethyl as the P1 group | |||||||||
Components | Protease | |||||||||
Keywords | HYDROLASE/INHIBITOR / ASPARTIC ACID PROTEASE / HIV-1 PROTEASE / INHIBITORS / pyridylpyrimidine / HYDROLASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Human immunodeficiency virus 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | |||||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Ghosh, A.K. / Weber, I.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2023 Title: Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation. Authors: Ghosh, A.K. / Mishevich, J.L. / Kovela, S. / Shaktah, R. / Ghosh, A.K. / Johnson, M. / Wang, Y.F. / Wong-Sam, A. / Agniswamy, J. / Amano, M. / Takamatsu, Y. / Hattori, S.I. / Weber, I.T. / Mitsuya, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fuj.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fuj.ent.gz | 95.8 KB | Display | PDB format |
PDBx/mmJSON format | 8fuj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/8fuj ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fuj | HTTPS FTP |
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-Related structure data
Related structure data | 8fuiC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: isolate BRU/LAI / Gene: pol / Plasmid: pJ414 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5RZ08, HIV-1 retropepsin |
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-Non-polymers , 6 types, 321 molecules
#2: Chemical | ChemComp-NA / | ||||||||
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#3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-Y9N / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.7 Å3/Da / Density % sol: 54.48 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.57M sodium chloride and 0.1 M sodium acetate, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.12→50 Å / Num. obs: 84494 / % possible obs: 93.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 6.894 Å2 / Rmerge(I) obs: 0.068 / Χ2: 0.037 / Net I/σ(I): 16.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→36.3 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.723 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.509 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→36.3 Å
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Refine LS restraints |
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