7R9W

LC3A in complex with Fragment 1-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands.

Steffek, M.Helgason, E.Popovych, N.Rouge, L.Bruning, J.M.Li, K.S.Burdick, D.J.Cai, J.Crawford, T.Xue, J.Decurtins, W.Fang, C.Grubers, F.Holliday, M.J.Langley, A.Petersen, A.Satz, A.L.Song, A.Stoffler, D.Strebel, Q.Tom, J.Y.K.Skelton, N.Staben, S.T.Wichert, M.Mulvihill, M.M.Dueber, E.C.

(2023) Biochemistry 62: 633-644

  • DOI: https://doi.org/10.1021/acs.biochem.1c00682
  • Primary Citation of Related Structures:  
    7R9W, 7R9Z, 7RA0

  • PubMed Abstract: 

    Autophagy-related proteins (Atgs) drive the lysosome-mediated degradation pathway, autophagy, to enable the clearance of dysfunctional cellular components and maintain homeostasis. In humans, this process is driven by the mammalian Atg8 (mAtg8) family of proteins comprising the LC3 and GABARAP subfamilies. The mAtg8 proteins play essential roles in the formation and maturation of autophagosomes and the capture of specific cargo through binding to the conserved LC3-interacting region (LIR) sequence within target proteins. Modulation of interactions of mAtg8 with its target proteins via small-molecule ligands would enable further interrogation of their function. Here we describe unbiased fragment and DNA-encoded library (DEL) screening approaches for discovering LC3 small-molecule ligands. Both strategies resulted in compounds that bind to LC3, with the fragment hits favoring a conserved hydrophobic pocket in mATG8 proteins, as detailed by LC3A-fragment complex crystal structures. Our findings demonstrate that the malleable LIR-binding surface can be readily targeted by fragments; however, rational design of additional interactions to drive increased affinity proved challenging. DEL libraries, which combine small, fragment-like building blocks into larger scaffolds, yielded higher-affinity binders and revealed an unexpected potential for reversible, covalent ligands. Moreover, DEL hits identified possible vectors for synthesizing fluorescent probes or bivalent molecules for engineering autophagic degradation of specific targets.


  • Organizational Affiliation

    Biochemical and Cellular Pharmacology, Genentech, 1 DNA Way, South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3A122Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H492 (Homo sapiens)
Explore Q9H492 
Go to UniProtKB:  Q9H492
PHAROS:  Q9H492
GTEx:  ENSG00000101460 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H492
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.761α = 90
b = 94.761β = 90
c = 32.81γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2023-02-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description