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Yorodumi- PDB-6uj4: Discovery of fragment-inspired heterocyclic benzenesulfonmides as... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uj4 | ||||||
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Title | Discovery of fragment-inspired heterocyclic benzenesulfonmides as inhibitors of the WDR5-MYC interaction | ||||||
Components | WD repeat domain 5 | ||||||
Keywords | TRANSCRIPTION / WDR5 / MYC / structure-based design / fragment screening | ||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / regulation of embryonic development / MLL1 complex / histone acetyltransferase complex / positive regulation of gluconeogenesis / methylated histone binding / transcription initiation-coupled chromatin remodeling / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å | ||||||
Authors | Zhao, B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: Discovery of WD Repeat-Containing Protein 5 (WDR5)-MYC Inhibitors Using Fragment-Based Methods and Structure-Based Design. Authors: Chacon Simon, S. / Wang, F. / Thomas, L.R. / Phan, J. / Zhao, B. / Olejniczak, E.T. / Macdonald, J.D. / Shaw, J.G. / Schlund, C. / Payne, W. / Creighton, J. / Stauffer, S.R. / Waterson, A.G. ...Authors: Chacon Simon, S. / Wang, F. / Thomas, L.R. / Phan, J. / Zhao, B. / Olejniczak, E.T. / Macdonald, J.D. / Shaw, J.G. / Schlund, C. / Payne, W. / Creighton, J. / Stauffer, S.R. / Waterson, A.G. / Tansey, W.P. / Fesik, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uj4.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uj4.ent.gz | 195.6 KB | Display | PDB format |
PDBx/mmJSON format | 6uj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uj4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6uj4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6uj4_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 6uj4_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/6uj4 ftp://data.pdbj.org/pub/pdb/validation_reports/uj/6uj4 | HTTPS FTP |
-Related structure data
Related structure data | 6uhyC 6uhzC 6uifC 6uikC 6ujhC 6ujjC 6ujlC 6uozC 6dy7S S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33492.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P61964 #2: Chemical | #3: Water | ChemComp-HOH / | 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: 2.18 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris 6.5, 0.2 M Ammonium acetate, 28% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→40 Å / Num. obs: 84598 / % possible obs: 97.6 % / Redundancy: 3.9 % / CC1/2: 0.986 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.052 / Rrim(I) all: 0.107 / Rsym value: 0.093 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.286 / Num. unique obs: 4025 / CC1/2: 0.835 / R split: 2.93 / Rpim(I) all: 0.169 / Rrim(I) all: 0.313 / Rsym value: 0.261 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DY7 Resolution: 1.53→29.809 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 16.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 44.05 Å2 / Biso mean: 9.505 Å2 / Biso min: 0.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→29.809 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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