Sex Hormone-binding globulin mutant E176K in complex with IPI

Experimental Data Snapshot

  • Resolution: 1.71 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

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Molecular interactions between sex hormone-binding globulin and nonsteroidal ligands that enhance androgen activity.

Round, P.Das, S.Wu, T.S.Wahala, K.Van Petegem, F.Hammond, G.L.

(2020) J Biol Chem 295: 1202-1211

  • DOI: https://doi.org/10.1074/jbc.RA119.011051
  • Primary Citation of Related Structures:  
    6PYA, 6PYB, 6PYF

  • PubMed Abstract: 

    Sex hormone-binding globulin (SHBG) determines the equilibrium between free and protein-bound androgens and estrogens in the blood and regulates their access to target tissues. Using crystallographic approaches and radiolabeled competitive binding-capacity assays, we report here how two nonsteroidal compounds bind to human SHBG, and how they influence androgen activity in cell culture. We found that one of these compounds, (-)3,4-divanillyltetrahydrofuran (DVT), present in stinging nettle root extracts and used as a nutraceutical, binds SHBG with relatively low affinity. By contrast, a synthetic compound, 3-(1H-imidazol-1-ylmethyl)-2phenyl-1H-indole (IPI), bound SHBG with an affinity similar to that of testosterone and estradiol. Crystal structures of SHBG in complex with DVT or IPI at 1.71-1.80 Å resolutions revealed their unique orientations in the SHBG ligand-binding pocket and suggested opportunities for the design of other nonsteroidal ligands of SHBG. As observed for estradiol but not testosterone, IPI binding to SHBG was reduced by ∼20-fold in the presence of zinc, whereas DVT binding was almost completely lost. Estradiol-dependent fibulin-2 interactions with SHBG similarly occurred for IPI-bound SHBG, but not with DVT-bound SHBG. Both DVT and IPI increased the activity of testosterone in a cell culture androgen reporter system by competitively displacing testosterone from SHBG. These findings indicate how nonsteroidal ligands of SHBG maybe designed to modulate the bioavailability of sex steroids.

  • Organizational Affiliation

    Department of Cellular & Physiological Sciences, The University of British Columbia, Vancouver, BC Canada V6T 1Z4.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sex hormone-binding globulin205Homo sapiensMutation(s): 1 
Gene Names: SHBG
UniProt & NIH Common Fund Data Resources
Find proteins for P04278 (Homo sapiens)
Explore P04278 
Go to UniProtKB:  P04278
GTEx:  ENSG00000129214 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04278
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P57 (Subject of Investigation/LOI)
Query on P57

Download Ideal Coordinates CCD File 
B [auth A]3-[(1H-imidazol-1-yl)methyl]-2-phenyl-1H-indole
C18 H15 N3
Query on CA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.71 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.241α = 90
b = 52.241β = 90
c = 147.87γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-25
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Database references
  • Version 1.2: 2020-02-12
    Changes: Database references