6VIF

Human LRH-1 ligand-binding domain bound to agonist cpd 15 and fragment of coregulator TIF-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development of a new class of liver receptor homolog-1 (LRH-1) agonists by photoredox conjugate addition.

Cornelison, J.L.Cato, M.L.Johnson, A.M.D'Agostino, E.H.Melchers, D.Patel, A.B.Mays, S.G.Houtman, R.Ortlund, E.A.Jui, N.T.

(2020) Bioorg Med Chem Lett 30: 127293-127293

  • DOI: 10.1016/j.bmcl.2020.127293
  • Primary Citation of Related Structures:  
    6VIF

  • PubMed Abstract: 
  • LRH-1 is a nuclear receptor that regulates lipid metabolism and homeostasis, making it an attractive target for the treatment of diabetes and non-alcoholic fatty liver disease. Building on recent structural information about ligand binding from our labs, we have designed a series of new LRH-1 agonists that further engage LRH-1 through added polar interactions ...

    LRH-1 is a nuclear receptor that regulates lipid metabolism and homeostasis, making it an attractive target for the treatment of diabetes and non-alcoholic fatty liver disease. Building on recent structural information about ligand binding from our labs, we have designed a series of new LRH-1 agonists that further engage LRH-1 through added polar interactions. While the current synthetic approach to this scaffold has, in large part, allowed for decoration of the agonist core, significant variation of the bridgehead substituent is mechanistically precluded. We have developed a new synthetic approach to overcome this limitation, identified that bridgehead substitution is necessary for LRH-1 activation, and described an alternative class of bridgehead substituents for effective LRH-1 agonist development. We determined the crystal structure of LRH-1 bound to a bridgehead-modified compound, revealing a promising opportunity to target novel regions of the ligand binding pocket to alter LRH-1 target gene expression.


    Related Citations: 
    • Towards automated crystallographic structure refinement with phenix.refine.
      Afonine, P.V., Grosse-Kunstleve, R.W., Echols, N., Headd, J.J., Moriarty, N.W., Mustyakimov, M., Terwilliger, T.C., Urzhumtsev, A., Zwart, P.H., Adams, P.D.
      (2012) Acta Crystallogr D Biol Crystallogr 68: 352
    • PHENIX: a comprehensive Python-based system for macromolecular structure solution.
      Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., McCoy, A.J., Moriarty, N.W., Oeffner, R., Read, R.J., Richardson, D.C., Richardson, J.S., Terwilliger, T.C., Zwart, P.H.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 213
    • MolProbity: More and better reference data for improved all-atom structure validation.
      Williams, C.J., Headd, J.J., Moriarty, N.W., Prisant, M.G., Videau, L.L., Deis, L.N., Verma, V., Keedy, D.A., Hintze, B.J., Chen, V.B., Jain, S., Lewis, S.M., Arendall 3rd, W.B., Snoeyink, J., Adams, P.D., Lovell, S.C., Richardson, J.S., Richardson, D.C.
      (2018) Protein Sci 27: 293
    • PDB_REDO: automated re-refinement of X-ray structure models in the PDB.
      Joosten, R.P., Salzemann, J., Bloch, V., Stockinger, H., Berglund, A.C., Blanchet, C., Bongcam-Rudloff, E., Combet, C., Da Costa, A.L., Deleage, G., Diarena, M., Fabbretti, R., Fettahi, G., Flegel, V., Gisel, A., Kasam, V., Kervinen, T., Korpelainen, E., Mattila, K., Pagni, M., Reichstadt, M., Breton, V., Tickle, I.J., Vriend, G.
      (2009) J Appl Crystallogr 42: 376
    • Features and development of Coot.
      Emsley, P., Lohkamp, B., Scott, W.G., Cowtan, K.
      (2010) Acta Crystallogr D Biol Crystallogr 66: 486

    Organizational Affiliation

    Department of Chemistry, Emory University, Atlanta, GA 30322, United States. Electronic address: njui@emory.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor subfamily 5 group A member 2 A245Homo sapiensMutation(s): 0 
Gene Names: NR5A2B1FCPFFTF
Find proteins for O00482 (Homo sapiens)
Explore O00482 
Go to UniProtKB:  O00482
NIH Common Fund Data Resources
PHAROS:  O00482
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 2 B14Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QY4
Query on QY4

Download Ideal Coordinates CCD File 
A
N-[(8beta,11alpha,12alpha)-8-{[methyl(phenyl)amino]methyl}-1,6:7,14-dicycloprosta-1(6),2,4,7(14)-tetraen-11-yl]sulfuric diamide
C28 H39 N3 O2 S
HMKCOKHJISOEPL-NSVAZKTRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.134α = 90
b = 46.134β = 90
c = 223.436γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



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 States5R01DK115213-03

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-10
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references