6VIF

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

PDB DOI: 10.2210/pdb6VIF/pdb

Classification: NUCLEAR PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-01-13 Released: 2020-06-10
Deposition Author(s): Cato, M.L., Ortlund, E.A.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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

Ligand Structure Quality Assessment

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

PubMed: 32631515 Search on PubMedSearch on PubMed Central
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. 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) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor subfamily 5 group A member 2	A	245	Homo sapiens	Mutation(s): 0 Gene Names: NR5A2, B1F, CPF, FTF
UniProt & NIH Common Fund Data Resources
Find proteins for O00482 (Homo sapiens) Explore O00482 Go to UniProtKB: O00482
PHAROS: O00482 GTEx: ENSG00000116833
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00482
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	B	14	Homo sapiens	Mutation(s): 0 Gene Names: NCOA2, BHLHE75, SRC2, TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596 Go to UniProtKB: Q15596
PHAROS: Q15596 GTEx: ENSG00000140396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15596
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QY4 (Subject of Investigation/LOI) Query on QY4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth 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