5G45

Ligand complex of RORg LBD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment Screening of Rorgammat Using Cocktail Crystallography: Identification of Simultaneous Binding of Multiple Fragments.

Xue, Y.Guo, H.Hillertz, P.

(2016) Chemmedchem 11: 1881

  • DOI: 10.1002/cmdc.201600242
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The retinoic-acid-related orphan receptor γ t (RORγt), as a master regulator of Th17 cell pathology, has become an attractive target for small-molecule drug discovery for the treatment of Th17-cell-related autoimmune diseases. A crystallographic frag ...

    The retinoic-acid-related orphan receptor γ t (RORγt), as a master regulator of Th17 cell pathology, has become an attractive target for small-molecule drug discovery for the treatment of Th17-cell-related autoimmune diseases. A crystallographic fragment screening was carried out for RORγt using the ligand binding domain. An overall hit rate of 5.5 % was obtained by screening 384 compounds in 96 cocktails. Five distinct hotspots were identified, and four regions of anchoring polar interactions were observed. In addition, significant induced fit was found for the binding of several fragments. Strikingly, a simultaneous binding of three fragments was revealed which presents interesting features including π-π stacking, multiple hydrogen bonds to the protein, and significant induced fit. Overall, the results offer a complete mapping of the ligand binding pocket and provide valuable inspiration in structure-based design for RORγt lead generation and optimization. The crystallographic screening also resulted in fragment hits that bind at the surface away from the ligand binding pocket. This surface site is near the plausible dimer interface by analogy with other nuclear receptor systems, which can provide initial hints to explore alternative ways to modulate RORγt through protein-protein interactions.


    Organizational Affiliation

    Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden. yafeng.xue@astrazeneca.com.,Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden.,Research and Development Information, AstraZeneca Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEAR RECEPTOR ROR-GAMMA
A
266Homo sapiensMutation(s): 0 
Gene Names: RORC (NR1F3, RORG, RZRG)
Find proteins for P51449 (Homo sapiens)
Go to Gene View: RORC
Go to UniProtKB:  P51449
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RORG
C
10Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
A7W
Query on A7W

Download SDF File 
Download CCD File 
A
8-AMINO-3-QUINOLINOL
C9 H8 N2 O
GLVURCUKRZAGQN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A7WKd: 500000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 62.220α = 90.00
b = 62.220β = 90.00
c = 154.060γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-03
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references