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Structure paper

TitleStructural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development.
Journal, issue, pagesNat. Chem. Biol., Vol. 12, Page 539-, Year 2016
Publish dateDec 22, 2014 (structure data deposition date)
AuthorsJohansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. ...Johansson, C. / Velupillai, S. / Tumber, A. / Szykowska, A. / Hookway, E.S. / Nowak, R.P. / Strain-Damerell, C. / Gileadi, C. / Philpott, M. / Burgess-Brown, N. / Wu, N. / Kopec, J. / Nuzzi, A. / Steuber, H. / Egner, U. / Badock, V. / Munro, S. / Lathangue, N.B. / Westaway, S. / Brown, J. / Athanasou, N. / Prinjha, R. / Brennan, P.E. / Oppermann, U.
External linksNat. Chem. Biol. / PubMed:27214403
MethodsX-ray diffraction
Resolution1.78 - 2.44 Å
Structure data

PDB-4uf0:
Crystal structure of JmjC domain of human histone demethylase UTY in complex with epitherapuetic compound 2-(((2-((2-(dimethylamino)ethyl) (ethyl)amino)-2-oxoethyl)amino)methyl)isonicotinic acid.
Method: X-RAY DIFFRACTION / Resolution: 1.78 Å

PDB-5a1f:
Crystal structure of the catalytic domain of PLU1 in complex with N-oxalylglycine.
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-5a3p:
Crystal structure of the catalytic domain of human PLU1 (JARID1B).
Method: X-RAY DIFFRACTION / Resolution: 2.008 Å

PDB-5a3t:
Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl) isonicotinic acid).
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-5a3w:
Crystal structure of human PLU-1 (JARID1B) in complex with Pyridine-2, 6-dicarboxylic Acid (PDCA)
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-5fpu:
Crystal structure of human JARID1B in complex with GSKJ1
Method: X-RAY DIFFRACTION / Resolution: 2.24 Å

PDB-5fpv:
Crystal structure of human JMJD2A in complex with compound KDOAM20A
Method: X-RAY DIFFRACTION / Resolution: 2.44 Å

PDB-5fun:
Crystal structure of human JARID1B in complex with GSK467
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-5fup:
Crystal structure of human JARID1B in complex with 2-oxoglutarate.
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-5fv3:
Crystal structure of human JARID1B construct c2 in complex with N- Oxalylglycine.
Method: X-RAY DIFFRACTION / Resolution: 2.37 Å

PDB-5fwj:
Crystal structure of human JARID1C in complex with KDM5-C49
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

Chemicals

ChemComp-FE2:
Unknown entry

ChemComp-MMK:
2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid

ChemComp-ZN:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-HOH:
WATER / Water

ChemComp-OGA:
N-OXALYLGLYCINE / inhibitor*YM / N-Oxalylglycine

ChemComp-MN:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION / Phosphate

ChemComp-EPE:
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / pH buffer*YM / HEPES

ChemComp-NI:
NICKEL (II) ION / Nickel

ChemComp-NA:
Unknown entry

ChemComp-PD2:
PYRIDINE-2,4-DICARBOXYLIC ACID / Lutidinic acid

ChemComp-K0I:
3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid

ChemComp-GZA:
2-[(1-benzyl-1H-pyrazol-4-yl)oxy]pyrido[3,4-d]pyrimidin-4(3H)-one

ChemComp-CL:
Unknown entry / Chloride

ChemComp-AKG:
2-OXOGLUTARIC ACID / Α-Ketoglutaric acid

ChemComp-DMS:
DIMETHYL SULFOXIDE / DMSO, precipitant*YM / Dimethyl sulfoxide

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsOXIDOREDUCTASE / LYSINE-SPECIFIC DEMETHYLASE 5B / TRANSCRIPTION / JMJD2A / KDM4A / JARID1B / PLU1 / LYSINE-SPECIFIC / LYSINE-SPECIFIC DEMETHYLASE 5C

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