6OQX

Human Liver Receptor Homolog-1 bound to the agonist 5N and a fragment of the Tif2 coregulator

  • Classification: TRANSCRIPTION
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2019-04-29 Released: 2019-08-28 
  • Deposition Author(s): Mays, S.G., Ortlund, E.A.
  • Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK); National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.004 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Development of the First Low Nanomolar Liver Receptor Homolog-1 Agonist through Structure-guided Design.

Mays, S.G.Flynn, A.R.Cornelison, J.L.Okafor, C.D.Wang, H.Wang, G.Huang, X.Donaldson, H.N.Millings, E.J.Polavarapu, R.Moore, D.D.Calvert, J.W.Jui, N.T.Ortlund, E.A.

(2019) J.Med.Chem. 62: 11022-11034

  • DOI: 10.1021/acs.jmedchem.9b00753
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • As a key regulator of metabolism and inflammation, the orphan nuclear hormone receptor, Liver Receptor Homolog-1 (LRH-1), has potential as a therapeutic target for diabetes, nonalcoholic fatty liver disease, and inflammatory bowel diseases. Discovery ...

    As a key regulator of metabolism and inflammation, the orphan nuclear hormone receptor, Liver Receptor Homolog-1 (LRH-1), has potential as a therapeutic target for diabetes, nonalcoholic fatty liver disease, and inflammatory bowel diseases. Discovery of LRH-1 modulators has been difficult, in part due to the tendency for synthetic compounds to bind unpredictably within the lipophilic binding pocket. Using a structure-guided approach, we exploited a newly-discovered polar interaction to lock agonists in a consistent orientation. This enabled the discovery of the first low nanomolar LRH-1 agonist, one hundred times more potent than the best previous modulator. We elucidate a novel mechanism of action that relies upon specific polar interactions deep in the LRH-1 binding pocket. In an organoid model of inflammatory bowel disease, the new agonist increases expression of LRH-1-conrolled steroidogenic genes and promotes anti-inflammatory gene expression changes. These studies constitute major progress in developing LRH-1 modulators with potential clinical utility.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor subfamily 5 group A member 2
A
245Homo sapiensMutation(s): 0 
Gene Names: NR5A2 (B1F, CPF, FTF)
Find proteins for O00482 (Homo sapiens)
Go to Gene View: NR5A2
Go to UniProtKB:  O00482
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
C
15Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N1V
Query on N1V

Download SDF File 
Download CCD File 
A
(8beta,11alpha,12alpha)-8-(1-phenylethenyl)-1,6:7,14-dicycloprosta-1,3,5,7(14)-tetraen-11-yl sulfamate
C28 H35 N O3 S
TUITYPXKFZGOFR-NSVAZKTRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.004 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.206 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 46.547α = 90.00
b = 46.547β = 90.00
c = 220.998γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK095750
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01DK114213
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesF31DK111171
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM008602

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-12-25
    Type: Author supporting evidence
  • Version 1.2: 2020-01-08
    Type: Database references