3VRU

VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands

Yoshimoto, N.Sakamaki, Y.Haeta, M.Kato, A.Inaba, Y.Itoh, T.Nakabayashi, M.Ito, N.Yamamoto, K.

(2012) J.Med.Chem. 55: 4373-4381

  • DOI: 10.1021/jm300230a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Previously, we reported that 22S-butyl-25,26,27-trinor-1α,24-dihydroxyvitamin D(3)2 represents a new class of antagonist for the vitamin D receptor (VDR). The crystal structure of the ligand-binding domain (LBD) of VDR complexed with 2 showed the for ...

    Previously, we reported that 22S-butyl-25,26,27-trinor-1α,24-dihydroxyvitamin D(3)2 represents a new class of antagonist for the vitamin D receptor (VDR). The crystal structure of the ligand-binding domain (LBD) of VDR complexed with 2 showed the formation of a butyl pocket to accommodate the 22-butyl group and insufficient interactions between ligand 2 and the C-terminus of VDR. Here, we designed and synthesized new analogues 5a-c and evaluated their biological activities to probe whether agonistic activity is recovered when the analogue restores interactions with the C-terminus of VDR. Analogues 5a-c exhibited full agonistic activity in transactivation. Interestingly, 5c, which bears a 24-diethyl group, completely recovered agonistic activity, although 3c and 4c act as an antagonist and a weak agonist, respectively. The crystal structures of VDR-LBD complexed with 3a, 4a, 5a, and 5c were solved, and the results confirmed that butyl pocket formation in VDR strongly affects the agonistic or antagonistic behaviors of ligands.


    Organizational Affiliation

    Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
271Rattus norvegicusMutation(s): 0 
Gene Names: Vdr (Nr1i1)
Find proteins for P13053 (Rattus norvegicus)
Go to UniProtKB:  P13053
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
13-meric peptide from Mediator of RNA polymerase II transcription subunit 1
C
13Homo sapiensMutation(s): 0 
Gene Names: MED1 (ARC205, CRSP1, CRSP200, DRIP205, DRIP230, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2)
Find proteins for Q15648 (Homo sapiens)
Go to Gene View: MED1
Go to UniProtKB:  Q15648
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YS3
Query on YS3

Download SDF File 
Download CCD File 
A
(1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol
C26 H42 O3
JLJBOAPFTSKXIR-PXIOBPQKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YS3IC50: 0.1 nM BINDINGMOAD
YS3IC50: 0.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 154.340α = 90.00
b = 42.290β = 95.89
c = 42.210γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-23
    Type: Initial release