Brand  (β version)

PDB ID: 5XPN

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Ligands
Code Name Style Show Link
8BO (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{S})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol PoSSuM
9RO (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-methoxy-hexan-2-yl]-7~{a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol PoSSuM
Non-standard Residues
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Structure summary

Code : 5XPN   PDBj   RCSB PDB   PDBe
Header : TRANSCRIPTION
Title : Crystal structure of VDR-LBD complexed with 25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3
Release Data : 2018-07-11
Compound :
mol_id molecule chains synonym
1 Vitamin D3 receptor A VDR,1,25-dihydroxyvitamin D3 receptor,Nuclear receptor subfamily 1 group I member 1
fragment: UNP residues 116-423
mutation: deletion mutant(residues 165-211)
mol_id molecule chains synonym
2 Mediator of RNA polymerase II transcription subunit 1 C Activator-recruited cofactor 205 kDa component,ARC205,Mediator complex subunit 1,Peroxisome proliferator-activated receptor-binding protein,PPAR-binding protein,Thyroid hormone receptor-associated protein complex 220 kDa component,Trap220,Thyroid receptor-interacting protein 2,TRIP-2,Vitamin D receptor-interacting protein complex component DRIP205,p53 regulatory protein RB18A
fragment: UNP residues 640-652
Source :
mol_id organism_scientific organism_common expression_system
1 Rattus norvegicus  (taxid:10116) Rat Escherichia coli  (taxid:562)
gene: Vdr, Nr1i1
mol_id organism_scientific organism_common expression_system
2 Homo sapiens  (taxid:9606) Human Synthetic construct  (taxid:32630)
gene: MED1, ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2
Authors : Kato, A., Itoh, T., Yamamoto, K.
Keywords : transcription, vitamin D3, VDR, VDRE, RXR, co-factors
Exp. method : X-RAY DIFFRACTION ( 1.96 Å )
Citation :

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

Kato, A.,Yamao, M.,Hashihara, Y.  et al.
(2017)  J. Med. Chem.  60 : 8394 - 8406

PubMed: 28954197
DOI: 10.1021/acs.jmedchem.7b00819

Reaction

Chain : A
UniProt : P13053 (VDR_RAT)
Reaction : -