9M12: Vitamin D3 receptor

Vitamin D receptor complex with a bis(3-ethylphenyl)dimethylsilane derivative. Determined by X-ray diffraction at 1.86 Å resolution. Released 11 Jun 2025.

Method: X-ray diffraction
Resolution: 1.86 Å
Organisms: Rattus norvegicus, Homo sapiens
Chains: 4
Atoms: 4,603
Mol. weight: 65.37 kDa
Ligands: A1L7Z
Released: 11 Jun 2025

Explore 9M12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M12 contains 30 α-helices and 6 β-strands across 4 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	223-241	19
α-helix	247-249	3
α-helix	252-271	20
α-helix	272-274	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	303-317	15
α-helix	323-334	12
α-helix	345-366	22
α-helix	371-401	31
α-helix	404-407	4
α-helix	412-418	7

Chain B: 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	223-243	21
α-helix	247-249	3
α-helix	252-270	19
α-helix	271-274	4
β-strand	275-276	2	2
β-strand	281-283	3	2
β-strand	290-291	2	2
α-helix	293-297	5
α-helix	303-318	16
α-helix	323-334	12
α-helix	345-366	22
α-helix	371-401	31
α-helix	404-407	4
α-helix	412-417	6

Chains C and D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	628-634	7

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>9M12_1 Vitamin D3 receptor (chains A, B)
GSHMGSPNSPLKDSLRPKLSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMDGSTGS
VTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSN
QSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAI
CIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEE
HSKQYRSLSFQPENSMKLTPLVLEVFGNEIS

Sequence of entity 2 (C, D), FASTA

>9M12_2 Mediator of RNA polymerase II transcription subunit 1 (chains C, D)
KNHPMLMNLLKDN

Ligands and cofactors

ID	Name	Formula	Copies
A1L7Z	(4~{S})-5-[2-ethyl-4-[[3-ethyl-4-(2-ethyl-2-oxidanyl-butoxy)phenyl]-dimethyl-si…	C29 H44 O6 Si	2

Primary citation

Structure-activity relationship and crystallographic analyses of non-secosteroidal vitamin D receptor ligands bearing diphenylsilane core as a hydrophobic pharmacophore. Mudiyanselage, H.N.T.N., Misawa, T., Ochiai, K. et al. Bioorg Med Chem (2025) 128:118261-118261. DOI 10.1016/j.bmc.2025.118261 · PubMed

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

9VOG 1.43 Å, Vitamin D receptor complex with a 5-{4-(m-carboran-1-yl)phenoxy}-4-hydroxypentanoic acid…
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

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