9DQA | pdb_00009dqa

Crystal structure of bovine RPE65 in complex with EYE-002


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.209 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.187 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rationally Designed, Short-Acting RPE65 Inhibitors for Visual Cycle-Associated Retinopathies.

Bassetto, M.Hu, Y.Li, B.Chen, X.Saraswat, V.Damacio, F.Smidak, R.Palczewski, K.Tochtrop, G.P.Kiser, P.D.

(2025) J Med Chem 68: 17638-17652

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01353
  • Primary Citation of Related Structures:  
    9DQA

  • PubMed Abstract: 

    The visual cycle is a metabolic pathway essential for visual function. The bisretinoid byproducts of this pathway can induce retinal toxicity, as occurs in Stargardt disease type 1 (STGD1). Emixustat, which inhibits bisretinoid production, is a visual cycle modulator (VCM) that targets RPE65. However, it causes visual impairment due to its unfavorable duration of action. Here, we report ester-containing analogs of emixustat that are susceptible to hydrolytic clearance and function as short-acting VCMs. We show that the esterase-mediated metabolism of these compounds can be tuned while maintaining high-affinity RPE65 targeting. Compounds 6 (EYE-002) and 7 (EYE-003) containing diethyl acetate and valproate esters, respectively, allowed faster recovery of visual cycle function compared to emixustat. These molecules protected against retinal degeneration in mouse models of photic retinopathy and STGD1. These data demonstrate that shorter attenuation of the visual cycle can therapeutically intervene in retinal diseases with fewer visual side effects compared to emixustat.


  • Organizational Affiliation
    • Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, California 92697, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinoid isomerohydrolase
A, B
533Bos taurusMutation(s): 0 
EC: 3.1.1.64 (PDB Primary Data), 5.3.3.22 (PDB Primary Data)
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BEO (Subject of Investigation/LOI)
Query on A1BEO

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
3-[(1R)-3-amino-1-hydroxypropyl]phenyl 2-ethylbutanoate
C15 H23 N O3
LERLIJBLOOAQOT-UHFFFAOYSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.209 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.187 (DCC) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 175.81α = 90
b = 175.81β = 90
c = 86.46γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Veterans Affairs (VA, United States)United StatesBX004939

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Database references