7T8H

G93A mutant of human SOD1 bound with MR6-26-2 in P21 space group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Ebselen analogues delay disease onset and its course in fALS by on-target SOD-1 engagement.

Watanabe, S.Amporndanai, K.Awais, R.Latham, C.Awais, M.O'Neill, P.M.Yamanaka, K.Hasnain, S.S.

(2024) Sci Rep 14: 12118-12118

  • DOI: https://doi.org/10.1038/s41598-024-62903-5
  • Primary Citation of Related Structures:  
    7T8E, 7T8F, 7T8G, 7T8H

  • PubMed Abstract: 

    Amyotrophic lateral sclerosis (ALS) selectively affects motor neurons. SOD1 is the first causative gene to be identified for ALS and accounts for at least 20% of the familial (fALS) and up to 4% of sporadic (sALS) cases globally with some geographical variability. The destabilisation of the SOD1 dimer is a key driving force in fALS and sALS. Protein aggregation resulting from the destabilised SOD1 is arrested by the clinical drug ebselen and its analogues (MR6-8-2 and MR6-26-2) by redeeming the stability of the SOD1 dimer. The in vitro target engagement of these compounds is demonstrated using the bimolecular fluorescence complementation assay with protein-ligand binding directly visualised by co-crystallography in G93A SOD1. MR6-26-2 offers neuroprotection slowing disease onset of SOD1 G93A mice by approximately 15 days. It also protected neuromuscular junction from muscle denervation in SOD1 G93A mice clearly indicating functional improvement.


  • Organizational Affiliation

    Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, 464-8601, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Superoxide dismutase [Cu-Zn]A,
B [auth F]
153Homo sapiensMutation(s): 1 
Gene Names: SOD1
EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q8E (Subject of Investigation/LOI)
Query on Q8E

Download Ideal Coordinates CCD File 
E [auth A],
I [auth F]
~{N}-[(6-methoxypyridin-3-yl)methyl]-2-selanyl-benzamide
C14 H14 N2 O2 Se
SGEBTMJCWYBJSF-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
K [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
H [auth F],
J [auth F]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.54α = 90
b = 68.478β = 105.024
c = 49.965γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesWA1128

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-06-05
    Changes: Database references