SMTL ID : 5xzf.1

Vitamin D receptor with a synthetic ligand ADRO1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 8J0: (1R,3S,5Z)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,6S)-6-(1-adamantyl)-6-oxidanyl-hex-4-yn-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol(Non-covalent)

8J0.1: 26 residues within 4Å: Chain A: Y.38, Y.42, L.71, L.74, A.75, V.78, S.81, I.112, I.115, R.118, S.119, S.122, W.130, C.132, Y.139, V.144, A.147, H.149, L.153, L.157, H.241, Y.245, L.258, V.262, F.266 Ligands: FMT.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.71, A:L.74, A:V.78, A:I.112, A:I.115, A:W.130, A:Y.139, A:V.144, A:L.153, A:L.157, A:Y.245, A:L.258, A:V.262, A:F.266 Hydrogen bonds: A:S.81, A:R.118, A:S.122, A:S.122, A:H.241

1 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 7 residues within 4Å: Chain A: T.37, Y.38, D.39, Y.80, K.84, R.118 Ligands: 8J0.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.39, A:D.39, A:R.118, A:R.118 Water bridges: A:D.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otero, R. et al., 25 S-Adamantyl-23-yne-26,27-dinor-1 alpha ,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex. J. Med. Chem. (2018)

Release Date

2018-07-25

Peptides

Vitamin D3 receptor: A
Mediator of RNA polymerase II transcription subunit 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Vitamin D3 receptor

Mediator of RNA polymerase II transcription subunit 1

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