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Yorodumi- PDB-5fpb: Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fpb | ||||||
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Title | Crystal structure of human KDM4D in complex with 2-1H-pyrazol-4-yloxy- 3H,4H-pyrido-3,4-d-pyrimidin-4-one | ||||||
Components | LYSINE-SPECIFIC DEMETHYLASE 4D | ||||||
Keywords | OXIDOREDUCTASE / INHIBITOR / LYSINE SPECIFIC HISTONE DEMETHYLASE / JMJD2D / KDM4D / JUMONJI | ||||||
Function / homology | Function and homology information positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / histone H3K9me2/H3K9me3 demethylase activity / [histone H3]-trimethyl-L-lysine9 demethylase / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / chromatin remodeling / inflammatory response / chromatin / nucleoplasm / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Chung, C. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Cell Penetrant Inhibitors of the Kdm4 and Kdm5 Families of Histone Lysine Demethylases. 1. 3-Amino-4-Pyridine Carboxylate Derivatives. Authors: Westaway, S.M. / Preston, A.G.S. / Barker, M.D. / Brown, F. / Brown, J.A. / Campbell, M. / Chung, C. / Diallo, H. / Douault, C. / Drewes, G. / Eagle, R. / Gordon, L. / Haslam, C. / Hayhow, T. ...Authors: Westaway, S.M. / Preston, A.G.S. / Barker, M.D. / Brown, F. / Brown, J.A. / Campbell, M. / Chung, C. / Diallo, H. / Douault, C. / Drewes, G. / Eagle, R. / Gordon, L. / Haslam, C. / Hayhow, T.G. / Humphreys, P.G. / Joberty, G. / Katso, R. / Kruidenier, L. / Leveridge, M. / Liddle, J. / Mosley, J. / Muelbaier, M. / Randle, R. / Rioja, I. / Rueger, A. / Seal, G.A. / Sheppard, R.J. / Singh, O. / Taylor, J. / Thomas, P. / Thomson, D. / Wilson, D.M. / Lee, K. / Prinjha, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fpb.cif.gz | 154.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpb.ent.gz | 127.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpb ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpb | HTTPS FTP |
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-Related structure data
-Links
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 38534.633 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 11-341 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q6B0I6, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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-Non-polymers , 5 types, 482 molecules
#2: Chemical | ChemComp-ZN / | ||
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#3: Chemical | ChemComp-CO / | ||
#4: Chemical | ChemComp-HA6 / | ||
#5: Chemical | ChemComp-SO4 / #6: 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: 2.48 Å3/Da / Density % sol: 50.37 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: 0.1M HEPES PH 7.4, 2.45M AMMONIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Feb 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→41.86 Å / Num. obs: 30844 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.91→2.01 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.9 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.91→31.15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.879 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.725 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→31.15 Å
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