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- PDB-5mw4: Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mw4 | ||||||
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Title | Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide] | ||||||
![]() | Histone-lysine N-methyltransferase, H3 lysine-79 specific![]() | ||||||
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Function / homology | ![]() histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Be, C. / Koch, E. / Gaul, C. / Stauffer, F. / Moebitz, H. / Scheufler, C. | ||||||
![]() | ![]() Title: Discovery of Potent, Selective, and Structurally Novel Dot1L Inhibitors by a Fragment Linking Approach. Authors: Mobitz, H. / Machauer, R. / Holzer, P. / Vaupel, A. / Stauffer, F. / Ragot, C. / Caravatti, G. / Scheufler, C. / Fernandez, C. / Hommel, U. / Tiedt, R. / Beyer, K.S. / Chen, C. / Zhu, H. / Gaul, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.1 KB | Display | ![]() |
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PDB format | ![]() | 219.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mvsC ![]() 5mw3C ![]() 1nw3S S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 38456.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8TEK3, ![]() #2: Chemical | #3: Chemical | ChemComp-SO4 / ![]() #4: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.96 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 0.92M Lithium sulfate monohydrate, 0.1M Ammonium sulfate, 0.1M Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.19→50 Å / Num. all: 55017 / Num. obs: 54968 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 47.35 Å2 / Rsym value: 0.097 / Net I/σ(I): 15.35 |
Reflection shell | Resolution: 2.19→2.25 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 2.05 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1nw3 Resolution: 2.19→45.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.159 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.158 / SU Rfree Blow DPI: 0.136 / SU Rfree Cruickshank DPI: 0.137
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Displacement parameters | Biso mean: 64.41 Å2
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Refine analyze | Luzzati coordinate error obs: 0.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.19→45.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.25 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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