SMTL ID : 2zmi.1

Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs: Structural Basis for Vitamin D Receptor Antagonism and/or Partial Agonism

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x TT2: (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]pent-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol(Non-covalent)

TT2.1: 22 residues within 4Å: Chain A: Y.38, Y.42, F.45, L.71, L.74, A.75, V.78, S.81, M.116, R.118, S.119, S.122, W.130, C.132, V.144, A.147, H.149, L.157, H.241, Y.245, L.248, L.258 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.38, A:L.71, A:A.75, A:V.78, A:W.130, A:W.130, A:V.144, A:L.157, A:Y.245, A:Y.245, A:L.248, A:L.258, A:L.258 Hydrogen bonds: A:R.118, A:S.122, A:S.122, A:H.241

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: L.263, N.268 No protein-ligand interaction detected (PLIP)

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

FMT.3: 5 residues within 4Å: Chain A: Q.200, S.204, Y.224, I.228, L.231 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.204, A:Y.224 Water bridges: A:Q.200, A:Q.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakabayashi, M. et al., Crystal structures of rat vitamin d receptor bound to adamantyl vitamin d analogs: structural basis for vitamin d receptor antagonism and partial agonism. J.Med.Chem. (2008)

Release Date

2008-09-02

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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