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- PDB-6ufx: WD repeat-containing protein 5 complexed with N-[(3,5-dimethoxyph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ufx | ||||||||||||
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Title | WD repeat-containing protein 5 complexed with N-[(3,5-dimethoxyphenyl)methyl]-4'-fluoro-5-{[(2E)-2-imino-3-methyl-2,3-dihydro-1H-imidazol-1-yl]methyl}-2'-methyl[1,1'-biphenyl]-3-carboxamide (compound 13) | ||||||||||||
![]() | WD repeat-containing protein 5 | ||||||||||||
![]() | GENE REGULATION/INHIBITOR / inhibitor / GENE REGULATION-INHIBITOR complex | ||||||||||||
Function / homology | ![]() 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 / mitotic spindle / PKMTs methylate histone lysines / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Neddylation / HATs acetylate histones / histone binding / regulation of cell cycle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Rietz, T.A. / Fesik, S.W. / Zhao, B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and Structure-Based Optimization of Potent and Selective WD Repeat Domain 5 (WDR5) Inhibitors Containing a Dihydroisoquinolinone Bicyclic Core. Authors: Tian, J. / Teuscher, K.B. / Aho, E.R. / Alvarado, J.R. / Mills, J.J. / Meyers, K.M. / Gogliotti, R.D. / Han, C. / Macdonald, J.D. / Sai, J. / Shaw, J.G. / Sensintaffar, J.L. / Zhao, B. / ...Authors: Tian, J. / Teuscher, K.B. / Aho, E.R. / Alvarado, J.R. / Mills, J.J. / Meyers, K.M. / Gogliotti, R.D. / Han, C. / Macdonald, J.D. / Sai, J. / Shaw, J.G. / Sensintaffar, J.L. / Zhao, B. / Rietz, T.A. / Thomas, L.R. / Payne, W.G. / Moore, W.J. / Stott, G.M. / Kondo, J. / Inoue, M. / Coffey, R.J. / Tansey, W.P. / Stauffer, S.R. / Lee, T. / Fesik, S.W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 77.2 KB | Display | ![]() |
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PDB format | ![]() | 53.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ucsC ![]() 3eg6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 33350.789 Da / Num. of mol.: 1 / Fragment: UNP residues 32-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-Q6S / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.6 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris or HEPES or Tris-HCl, pH 6.0-8.0, 0.2 M ammonium acetate, 20-30% PEG3350 PH range: 6.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 10, 2019 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 20876 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.048 / Rrim(I) all: 0.169 / Rsym value: 0.108 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2→2.03 Å / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 3.41 / Num. unique obs: 1005 / CC1/2: 0.762 / Rpim(I) all: 0.319 / Rrim(I) all: 1.085 / Rsym value: 1.032 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3EG6 Resolution: 2.015→28.746 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.09
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.56 Å2 / Biso mean: 23.091 Å2 / Biso min: 10.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.015→28.746 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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