Crystal structure of RPE65 in complex with compound 16e and palmitate

  • Classification: HYDROLASE
  • Organism(s): Bos taurus
  • Mutation(s): Yes 

  • Deposited: 2022-07-12 Released: 2023-05-24 
  • Deposition Author(s): Bassetto, M., Kiser, P.D.
  • Funding Organization(s): Department of Veterans Affairs (VA, United States)

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Tuning the Metabolic Stability of Visual Cycle Modulators through Modification of an RPE65 Recognition Motif.

Bassetto, M.Zaluski, J.Li, B.Zhang, J.Badiee, M.Kiser, P.D.Tochtrop, G.P.

(2023) J Med Chem 66: 8140-8158

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00461
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In the eye, the isomerization of all- trans -retinal to 11- cis -retinal is accomplished by a metabolic pathway termed the visual cycle that is critical for vision. RPE65 is the essential trans - cis isomerase of this pathway. Emixustat, a retinoid-mimetic RPE65 inhibitor, was developed as a therapeutic visual cycle modulator and used for the treatment of retinopathies. However, pharmacokinetic liabilities limit its further development including: (1) metabolic deamination of the γ-amino-α-aryl alcohol, which mediates targeted RPE65 inhibition, and (2) unwanted long-lasting RPE65 inhibition. We sought to address these issues by more broadly defining the structure-activity relationships of the RPE65 recognition motif via the synthesis of a family of novel derivatives, which were tested in vitro and in vivo for RPE65 inhibition. We identified a potent secondary amine derivative with resistance to deamination and preserved RPE65 inhibitory activity. Our data provide insights into activity-preserving modifications of the emixustat molecule that can be employed to tune its pharmacological properties.

  • Organizational Affiliation

    Department of Physiology and Biophysics, School of Medicine, University of California - Irvine, Irvine, California 92697, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoid isomerohydrolase533Bos taurusMutation(s): 1 
EC: (PDB Primary Data), (PDB Primary Data)
Find proteins for Q28175 (Bos taurus)
Explore Q28175 
Go to UniProtKB:  Q28175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28175
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.82α = 90
b = 176.82β = 90
c = 86.19γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Department of Veterans Affairs (VA, United States)--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2023-12-13
    Changes: Database references