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Open data
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Basic information
Entry | Database: PDB / ID: 7vqs | ||||||
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Title | Crystal structure of LSD1 in complex with compound 4 | ||||||
![]() | Lysine-specific histone demethylase 1A | ||||||
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Function / homology | ![]() guanine metabolic process / protein demethylation / [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase / FAD-dependent H3K4me/H3K4me3 demethylase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Niwa, H. / Koda, Y. / Sato, S. / Yamamoto, H. / Koyama, H. / Umehara, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles. Authors: Koda, Y. / Sato, S. / Yamamoto, H. / Niwa, H. / Watanabe, H. / Watanabe, C. / Sato, T. / Nakamura, K. / Tanaka, A. / Shirouzu, M. / Honma, T. / Fukami, T. / Koyama, H. / Umehara, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.1 KB | Display | ![]() |
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PDB format | ![]() | 223.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7vqtC ![]() 7vquC ![]() 6kgpS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 74333.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O60341, [histone H3]-N6,N6-dimethyl-L-lysine4 FAD-dependent demethylase | ||||||||
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#2: Chemical | ChemComp-GOL / ![]() #3: Chemical | ChemComp-TLA / | ![]() #4: Chemical | ChemComp-7UQ / | #5: Chemical | ChemComp-FAD / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.59 Å3/Da / Density % sol: 65.72 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Feb 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.94→48 Å / Num. obs: 23702 / % possible obs: 100 % / Redundancy: 18.3 % / Biso Wilson estimate: 86.36 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.035 / Rrim(I) all: 0.15 / Rsym value: 0.146 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.94→3.12 Å / Redundancy: 18.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3765 / CC1/2: 0.745 / Rpim(I) all: 0.536 / Rrim(I) all: 2.336 / Rsym value: 2.273 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 6KGP Resolution: 2.94→48 Å / SU ML: 0.4476 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 28.8347 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 98.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→48 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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