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Yorodumi- PDB-6d9x: Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6d9x | ||||||
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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 | dna binding protein/inhibitor / WDR5 / WIN-site / fragment screening / structure-based design / mixed-lineage leukemia / DNA BINDING PROTEIN / dna binding protein-inhibitor complex | ||||||
Function / homology | Function and homology information MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation ...MLL3/4 complex / Set1C/COMPASS complex / MLL1/2 complex / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / : / Cardiogenesis / histone methyltransferase complex / regulation of tubulin deacetylation / regulation of cell division / Formation of WDR5-containing histone-modifying complexes / MLL1 complex / regulation of embryonic development / histone acetyltransferase complex / positive regulation of gluconeogenesis / transcription initiation-coupled chromatin remodeling / methylated histone binding / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å | ||||||
Authors | Phan, J. / Fesik, S.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Med. Chem. / Year: 2018 Title: Discovery of Potent 2-Aryl-6,7-dihydro-5 H-pyrrolo[1,2- a]imidazoles as WDR5-WIN-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design. Authors: Wang, F. / Jeon, K.O. / Salovich, J.M. / Macdonald, J.D. / Alvarado, J. / Gogliotti, R.D. / Phan, J. / Olejniczak, E.T. / Sun, Q. / Wang, S. / Camper, D. / Yuh, J.P. / Shaw, J.G. / Sai, J. / ...Authors: Wang, F. / Jeon, K.O. / Salovich, J.M. / Macdonald, J.D. / Alvarado, J. / Gogliotti, R.D. / Phan, J. / Olejniczak, E.T. / Sun, Q. / Wang, S. / Camper, D. / Yuh, J.P. / Shaw, J.G. / Sai, J. / Rossanese, O.W. / Tansey, W.P. / Stauffer, S.R. / 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 | 6d9x.cif.gz | 77.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6d9x.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 6d9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9x ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9x | HTTPS FTP |
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-Related structure data
Related structure data | 6daiC 6dakC 6darC 6dasC 4y7rS 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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Unit cell |
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-Components
#1: Protein | Mass: 34390.992 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-FZM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M Bis-Tris pH 6.0, 0.2 M ammonium acetate, 28% to 32% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. obs: 25685 / % possible obs: 99.1 % / Redundancy: 8 % / Rpim(I) all: 0.027 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.83→1.86 Å / Redundancy: 6.5 % / Num. unique obs: 1192 / Rpim(I) all: 0.264 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y7R Resolution: 1.83→29.443 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.83→29.443 Å
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Refine LS restraints |
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LS refinement shell |
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