Crystal Structure of human JMJD2D complexed with KDOPP7

Summary for 5F5C

DescriptorLysine-specific demethylase 4D, ZINC ION, NICKEL (II) ION, ... (7 entities in total)
Functional Keywordsdouble-stranded beta helix, demethylase, oxygenase, oxidoreductase, structural genomics, structural genomics consortium, sgc
Biological sourceHomo sapiens (Human)
Cellular locationNucleus  Q6B0I6
Total number of polymer chains1
Total molecular weight41006.28
Primary citation
Bavetsias, V.,Lanigan, R.M.,Ruda, G.F.,Atrash, B.,McLaughlin, M.G.,Tumber, A.,Mok, N.Y.,Le Bihan, Y.V.,Dempster, S.,Boxall, K.J.,Jeganathan, F.,Hatch, S.B.,Savitsky, P.,Velupillai, S.,Krojer, T.,England, K.S.,Sejberg, J.,Thai, C.,Donovan, A.,Pal, A.,Scozzafava, G.,Bennett, J.M.,Kawamura, A.,Johansson, C.,Szykowska, A.,Gileadi, C.,Burgess-Brown, N.A.,von Delft, F.,Oppermann, U.,Walters, Z.,Shipley, J.,Raynaud, F.I.,Westaway, S.M.,Prinjha, R.K.,Fedorov, O.,Burke, R.,Schofield, C.J.,Westwood, I.M.,Bountra, C.,Muller, S.,van Montfort, R.L.,Brennan, P.E.,Blagg, J.
8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent, Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine Demethylase Inhibitors.
J.Med.Chem., 59:1388-1409, 2016
PubMed: 26741168 (PDB entries with the same primary citation)
DOI: 10.1021/acs.jmedchem.5b01635
MImport into Mendeley
Experimental method

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.217402.9%0.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5f5c
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Molmil generated image of 5f5c
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Molmil generated image of 5f5c
rotated about y axis by 90°