Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3

Summary for 5XPL

DescriptorVitamin D3 receptor, Nuclear receptor coactivator 2, (4~{S})-4-[(1~{R})-1-[(1~{R},3~{a}~{S},4~{E},7~{a}~{R})-7~{a}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl)cyclohexylidene]ethylidene]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(4-hydroxyphenyl)octan-1-one, ... (4 entities in total)
Functional Keywordstranscription, vitamin d3, vdr, vdre, rxr, co-factors, src2-3, antagonist
Biological sourceRattus norvegicus (Rat)
Total number of polymer chains2
Total molecular weight32723.65
Kato, A.,Itoh, T.,Yamamoto, K. (deposition date: 2017-06-03, release date: 2018-06-06, Last modification date: 2018-06-13)
Primary citation
Kato, A.,Yamao, M.,Hashihara, Y.,Ishida, H.,Itoh, T.,Yamamoto, K.
Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action
J. Med. Chem., 60:8394-8406, 2017
PubMed: 28954197 (PDB entries with the same primary citation)
DOI: 10.1021/acs.jmedchem.7b00819
MImport into Mendeley
Experimental method

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers 0.25460 1.3% 3.2%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution
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PDB entries from 2020-10-28