8G9V

Crystal structures of 17-beta-hydroxysteroid dehydrogenase 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
17-beta-hydroxysteroid dehydrogenase 13
A, B, C, D, E
A, B, C, D, E, F, G, H
315Homo sapiensMutation(s): 4 
Gene Names: HSD17B13SCDR9SDR16C3HMFN0376UNQ497/PRO1014
EC: 1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z5P4 (Homo sapiens)
Explore Q7Z5P4 
Go to UniProtKB:  Q7Z5P4
PHAROS:  Q7Z5P4
GTEx:  ENSG00000170509 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z5P4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
CA [auth E]
FA [auth F]
I [auth A]
KA [auth G]
N [auth B]
CA [auth E],
FA [auth F],
I [auth A],
KA [auth G],
N [auth B],
OA [auth H],
R [auth C],
Y [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
CE1
Query on CE1

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth E],
K [auth A],
T [auth C]
O-DODECANYL OCTAETHYLENE GLYCOL
C28 H58 O9
YYELLDKEOUKVIQ-UHFFFAOYSA-N
YYC (Subject of Investigation/LOI)
Query on YYC

Download Ideal Coordinates CCD File 
DA [auth E]
GA [auth F]
J [auth A]
LA [auth G]
O [auth B]
DA [auth E],
GA [auth F],
J [auth A],
LA [auth G],
O [auth B],
PA [auth H],
S [auth C],
Z [auth D]
4-{[2,5-dimethyl-3-(4-methylbenzene-1-sulfonyl)benzene-1-sulfonyl]amino}benzoic acid
C22 H21 N O6 S2
VUONIWZYCHRGQL-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth E]
HA [auth F]
IA [auth F]
JA [auth F]
L [auth A]
EA [auth E],
HA [auth F],
IA [auth F],
JA [auth F],
L [auth A],
M [auth A],
MA [auth G],
NA [auth G],
P [auth B],
Q [auth B],
QA [auth H],
RA [auth H],
SA [auth H],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.15α = 90
b = 161.56β = 95.05
c = 100.77γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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