8G93

Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis of lipid-droplet localization of 17-beta-hydroxysteroid dehydrogenase 13.

Liu, S.Sommese, R.F.Nedoma, N.L.Stevens, L.M.Dutra, J.K.Zhang, L.Edmonds, D.J.Wang, Y.Garnsey, M.Clasquin, M.F.

(2023) Nat Commun 14: 5158-5158

  • DOI: https://doi.org/10.1038/s41467-023-40766-0
  • Primary Citation of Related Structures:  
    8G84, 8G89, 8G93, 8G9V

  • PubMed Abstract: 

    Hydroxysteroid 17-beta-dehydrogenase 13 (HSD17B13) is a hepatic lipid droplet-associated enzyme that is upregulated in patients with non-alcoholic fatty liver disease. Recently, there have been several reports that predicted loss of function variants in HSD17B13 protect against the progression of steatosis to non-alcoholic steatohepatitis with fibrosis and hepatocellular carcinoma. Here we report crystal structures of full length HSD17B13 in complex with its NAD + cofactor, and with lipid/detergent molecules and small molecule inhibitors from two distinct series in the ligand binding pocket. These structures provide insights into a mechanism for lipid droplet-associated proteins anchoring to membranes as well as a basis for HSD17B13 variants disrupting function. Two series of inhibitors interact with the active site residues and the bound cofactor similarly, yet they occupy different paths leading to the active site. These structures provide ideas for structure-based design of inhibitors that may be used in the treatment of liver disease.


  • Organizational Affiliation

    Medicine Design, Pfizer Inc, Groton, CT, 06340, USA. Shenping.Liu@pfizer.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxysteroid 17-beta dehydrogenase 13
A, B
315Canis lupus familiarisMutation(s): 4 
Gene Names: HSD17B13
UniProt
Find proteins for A0A8I3RYU0 (Canis lupus familiaris)
Explore A0A8I3RYU0 
Go to UniProtKB:  A0A8I3RYU0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8I3RYU0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.73α = 90
b = 186.32β = 90
c = 65.32γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-08-09 
  • Deposition Author(s): Liu, S.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references