4YMQ

X-ray co-structure of nuclear receptor ROR-GAMMAT + SRC2 peptide with a benzothiadiazole dioxide inverse agonist


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of 1,3-dihydro-2,1,3-benzothiadiazole 2,2-dioxide analogs as new RORC modulators.

Muegge, I.Collin, D.Cook, B.Hill-Drzewi, M.Horan, J.Kugler, S.Labadia, M.Li, X.Smith, L.Zhang, Y.

(2015) Bioorg Med Chem Lett 25: 1892-1895

  • DOI: 10.1016/j.bmcl.2015.03.042
  • Primary Citation of Related Structures:  
    4YMQ

  • PubMed Abstract: 
  • Structure-based and pharmacophore-based virtual screening in combination with combinatorial chemistry and X-ray crystallography led to the discovery of a new class of benzothiadiazole dioxide analogs with functional activity as RORC inverse agonists. The early RORC SAR compound 14 exhibited RORC inhibition in a cell based reporter gene assay of 5 ...

    Structure-based and pharmacophore-based virtual screening in combination with combinatorial chemistry and X-ray crystallography led to the discovery of a new class of benzothiadiazole dioxide analogs with functional activity as RORC inverse agonists. The early RORC SAR compound 14 exhibited RORC inhibition in a cell based reporter gene assay of 5.7 μM and bound to RORC with an affinity of 1.6 μM in a fluorescence polarization assay displacing a ligand binding site probe. Crystallography confirmed the binding mode of the compound in the ligand binding domain displaying the engagement of a novel sub pocket close to Ser404. Subsequent optimization yielded compounds with enhanced RORC inverse agonist activity. The most active compound 19 showed an IC50 of 440 nM in a human PBMC assay.


    Organizational Affiliation

    Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, PO Box 368, Ridgefield, CT 06877-0368, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor ROR-gamma A280Homo sapiensMutation(s): 0 
Gene Names: RORCNR1F3RORGRZRG
Find proteins for P51449 (Homo sapiens)
Explore P51449 
Go to UniProtKB:  P51449
NIH Common Fund Data Resources
PHAROS:  P51449
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZBD
Query on ZBD

Download Ideal Coordinates CCD File 
A
4-{3-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)benzyl]-2,2-dioxido-2,1,3-benzothiadiazol-1(3H)-yl}-N-[(2R)-4-hydroxybutan-2-yl]-N-methylbutanamide
C25 H29 F6 N3 O5 S
SULHDXFOLGGHOR-QGZVFWFLSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ZBDKd:  1600   nM  BindingDB
ZBDIC50:  5700   nM  BindingDB
ZBDIC50:  5400   nM  BindingDB
ZBDKd:  1600   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.909α = 90
b = 61.909β = 90
c = 156.965γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-03-07 
  • Released Date: 2015-04-22 
  • Deposition Author(s): li, X.

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-04-29
    Changes: Database references