7ELG

LC3B modificated with a covalent probe


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Inhibition of autophagy by a small molecule through covalent modification of LC3.

Fan, S.Yue, L.Wan, W.Zhang, Y.Zhang, B.Otomo, C.Li, Q.Lin, T.Hu, J.Xu, P.Zhu, M.Tao, H.Chen, Z.Li, L.Ding, H.Yao, Z.Lu, J.Wen, Y.Zhang, N.Tan, M.Chen, K.Xie, Y.Otomo, T.Zhou, B.Jiang, H.Dang, Y.Luo, C.

(2021) Angew Chem Int Ed Engl 

  • DOI: 10.1002/anie.202109464
  • Primary Citation of Related Structures:  
    7ELG

  • PubMed Abstract: 
  • The autophagic ubiquitin-like protein LC3 functions through interactions with LC3-interaction regions (LIRs) of other autophagy proteins including autophagy receptors, which stands out as a promising protein-protein interaction (PPI) target for the intervention of autophagy ...

    The autophagic ubiquitin-like protein LC3 functions through interactions with LC3-interaction regions (LIRs) of other autophagy proteins including autophagy receptors, which stands out as a promising protein-protein interaction (PPI) target for the intervention of autophagy. Post-translational modifications like acetylation of Lys49 on the LIR-interacting surface could disrupt the interaction, offering an opportunity to design covalent small molecules interfering the interface. Through screening covalent compounds, we discover a small molecule modulator of LC3A/B that covalently modifies LC3A/B protein at Lys49. Activity-based protein profiling (ABPP) based evaluations reveal that a derivative molecule DC-LC3in-D5 exhibits a potent covalent reactivity and selectivity to LC3A/B in HeLa cells. DC-LC3in-D5 compromises LC3B lipidation in vitro and in HeLa cells, leading to deficiency in the formation of autophagic structures and autophagic substrate degradation. DC-LC3in-D5 could serve as a powerful tool for autophagy research as well as for therapeutic interventions.


    Organizational Affiliation

    Chongqing Medical University, Center for Novel Target and Therapeutic Intervention, CHINA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Microtubule-associated proteins 1A/1B light chain 3BA123Homo sapiensMutation(s): 0 
Gene Names: MAP1LC3BMAP1ALC3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZQ8 (Homo sapiens)
Explore Q9GZQ8 
Go to UniProtKB:  Q9GZQ8
PHAROS:  Q9GZQ8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8Z6 (Subject of Investigation/LOI)
Query on 8Z6

Download Ideal Coordinates CCD File 
B [auth A]2-methylidene-5-thiophen-2-yl-cyclohexane-1,3-dione
C11 H10 O2 S
UVAAMJSQZGJWHM-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.108α = 90
b = 54.766β = 90
c = 60.792γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-04-10 
  • Released Date: 2021-10-13 
  • Deposition Author(s): Fan, S., Wan, W.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81625022
National Natural Science Foundation of China (NSFC)China91853205
National Natural Science Foundation of China (NSFC)China81821005

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release