|Entry||Database: PDB / ID: 6e1y|
|Title||Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site Inhibitors Using Fragment-Based Methods and Structure-Based Design|
|Components||WD repeat-containing protein 5|
|Keywords||gene regulation/inhibitor / WDR5 / WIN-site / fragment screening / structure-based design / mixed-lineage leukemia / DNA BINDING PROTEIN / dna binding protein-inhibitor complex / GENE REGULATION / gene regulation-inhibitor complex|
|Function / homology|
Function and homology information
regulation of histone deacetylation / Set1C/COMPASS complex / MLL3/4 complex / MLL1/2 complex / ATAC complex / regulation of dosage compensation by inactivation of X chromosome / histone H3-K14 acetylation / histone H4-K16 acetylation / NSL complex / histone H4-K5 acetylation ...regulation of histone deacetylation / Set1C/COMPASS complex / MLL3/4 complex / MLL1/2 complex / ATAC complex / regulation of dosage compensation by inactivation of X chromosome / histone H3-K14 acetylation / histone H4-K16 acetylation / NSL complex / histone H4-K5 acetylation / histone H4-K8 acetylation / regulation of tubulin deacetylation / negative regulation of histone H3-K4 methylation / histone H3-K4 methylation / histone methyltransferase complex / regulation of cell division / positive regulation of histone H3-K4 methylation / MLL1 complex / regulation of embryonic development / positive regulation of gluconeogenesis / histone acetyltransferase complex / histone H3 acetylation / transcription initiation-coupled chromatin remodeling / methylated histone binding / skeletal system development / gluconeogenesis / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RMTs methylate histone arginines / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / mitotic spindle / neuron projection development / 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 / nucleoplasm / nucleus
Similarity search - Function
YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats ...YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats circular profile. / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-HLM / WD repeat-containing protein 5
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.219 Å|
|Authors||Phan, J. / Fesik, S.W.|
|Funding support|| United States, 1items |
|Citation||Journal: Cell Rep / Year: 2019|
Title: Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity.
Authors: Aho, E.R. / Wang, J. / Gogliotti, R.D. / Howard, G.C. / Phan, J. / Acharya, P. / Macdonald, J.D. / Cheng, K. / Lorey, S.L. / Lu, B. / Wenzel, S. / Foshage, A.M. / Alvarado, J. / Wang, F. / ...Authors: Aho, E.R. / Wang, J. / Gogliotti, R.D. / Howard, G.C. / Phan, J. / Acharya, P. / Macdonald, J.D. / Cheng, K. / Lorey, S.L. / Lu, B. / Wenzel, S. / Foshage, A.M. / Alvarado, J. / Wang, F. / Shaw, J.G. / Zhao, B. / Weissmiller, A.M. / Thomas, L.R. / Vakoc, C.R. / Hall, M.D. / Hiebert, S.W. / Liu, Q. / Stauffer, S.R. / Fesik, S.W. / Tansey, W.P.
|Structure viewer||Molecule: |
Downloads & links
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
A: WD repeat-containing protein 5
B: WD repeat-containing protein 5
Mass: 34390.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR5, BIG3 / Production host: Escherichia coli (E. coli) / References: UniProt: P61964
|#2: Chemical||#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 %|
|Crystal grow||Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 |
Details: 0.1 M Bis-Tris pH 6.0 or Hepes pH 7.5, 0.2 M ammonium acetate, 28% to 32% PEG3350
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å|
|Detector||Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2018|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.98 Å / Relative weight: 1|
|Reflection||Resolution: 1.219→50 Å / Num. obs: 173496 / % possible obs: 94.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.68|
|Reflection shell||Resolution: 1.22→1.24 Å / Rmerge(I) obs: 0.292|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 6D9X
Resolution: 1.219→29.016 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.65
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å|
|Refinement step||Cycle: LAST / Resolution: 1.219→29.016 Å|
|Refine LS restraints|
|LS refinement shell|
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