8F8M

LRH-1 bound to small molecule Tet and fragment of coactivator Tif2

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

  • Deposited: 2022-11-22 Released: 2023-11-29 
  • 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), American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Isosteric improvements to liver receptor homolog-1 small molecule modulators

Cato, M.L., Abraham, S.M., Spurlin, R.M., Flynn, A.R., Colucci, J.K., D'Agostino, E.H., Johnson, A.M., Jui, N.T., Ortlund, E.A.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 5 group A member 2246Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00482
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor coactivator 214Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XKE (Subject of Investigation/LOI)
Query on XKE
Download Ideal Coordinates CCD File 
C [auth A](1~{R},3~{a}~{R},6~{a}~{R})-4-phenyl-3~{a}-(1-phenylethenyl)-5-[9-(1~{H}-1,2,3,4-tetrazol-5-yl)nonyl]-2,3,6,6~{a}-tetrahydro-1~{H}-pentalen-1-ol
C32 H40 N4 O
KWRMCWKEHBRILN-LBRLCBGXSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.161α = 90
b = 89.161β = 90
c = 105.692γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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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 StatesF31-DK122745
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)United StatesR01-DK115213
American Heart AssociationUnited States20PRE35200311
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008367-29
National Science Foundation (NSF, United States)United StatesDGE-1444932

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release