9VOG: Vitamin D3 receptor

Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid derivative. Determined by X-ray diffraction at 1.43 Å resolution. Released 3 Dec 2025.

Method: X-ray diffraction
Resolution: 1.43 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 2
Atoms: 2,360
Mol. weight: 32.76 kDa
Ligands: A1MAV
Released: 3 Dec 2025

Explore 9VOG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VOG contains 15 α-helices and 3 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	126-142	17
α-helix	148-152	5
α-helix	154-156	3
α-helix	223-242	20
α-helix	247-249	3
α-helix	252-270	19
α-helix	271-273	3
β-strand	275-276	2	1
β-strand	281-283	3	1
β-strand	290-291	2	1
α-helix	293-297	5
α-helix	303-319	17
α-helix	323-334	12
α-helix	345-366	22
α-helix	375-401	27
α-helix	404-407	4
α-helix	412-418	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	628-633	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vitamin D3 receptor	A	protein	271	Rattus norvegicus	P13053 (AlphaFold model)
Mediator of RNA polymerase II transcription subunit 1	C	protein	13	Homo sapiens	Q15648 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9VOG_1 Vitamin D3 receptor (chains A)
GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGS
VTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSN
QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEE
HSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (C), FASTA

>9VOG_2 Mediator of RNA polymerase II transcription subunit 1 (chains C)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
A1MAV	(S)-5-[4-{7-(4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl)-1,7-dicarba…	C22 H28 B10 F6 O5	1

Primary citation

Design, synthesis and structural development of nonsecosteroidal VDR ligands based on the C,C'-diphenyl-m-carborane scaffold. Mudiyanselage, H.N.T.N., Misawa, T., Ochiai, K. et al. Eur J Med Chem (2025) 302:118320-118320. DOI 10.1016/j.ejmech.2025.118320 · PubMed

Other PDB entries of the same protein (UniProt P13053 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9M1D 1.44 Å, Vitamin D receptor complex with a methyldiphenylpropylsilane derivative
3VTC 1.5 Å, Crystal structure of rat vitamin D receptor bound to a partial agonist…
3VT7 1.65 Å, Crystal structures of rat VDR-LBD with W282R mutation
9M1C 1.67 Å, Vitamin D receptor complex with a triphenylpropylsilane derivative
9M13 1.68 Å, Vitamin D receptor complex with a dimethyldiphenylsilane derivative
2ZMI 1.7 Å, Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs:…
3VT3 1.7 Å, Crystal structures of rat VDR-LBD with R270L mutation
2O4J 1.74 Å, Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII…
9VOL 1.75 Å, Vitamin D receptor complex with a 4-{4-(m-carboran-1-yl)-2-methylphenoxy}butanoic acid…
9M1B 1.77 Å, Vitamin D receptor complex with a diphenydipropylsilane derivative
9M1A 1.78 Å, Vitamin D receptor complex with a diethyldiphenylsilane derivative
3W0H 1.8 Å, Crystal Structure of Rat VDR Ligand Binding Domain in Complex with Novel…

Browse structure collections

About this viewer

MolViewer shows 9VOG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.