6A9O

Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential for amyotrophic lateral sclerosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential for amyotrophic lateral sclerosis.

Manjula, R.Unni, S.Wright, G.S.A.Bharath M M, S.Padmanabhan, B.

(2019) J.Biomol.Struct.Dyn. 37: 3936-3946

  • DOI: 10.1080/07391102.2018.1531787

  • PubMed Abstract: 
  • Formation of Cu, Zn superoxide dismutase 1 (SOD1) protein inclusions within motor neurons is one of the principal characteristics of SOD1-related amyotrophic lateral sclerosis (ALS). A hypothesis as to the nature of SOD1 aggregation implicates oxidat ...

    Formation of Cu, Zn superoxide dismutase 1 (SOD1) protein inclusions within motor neurons is one of the principal characteristics of SOD1-related amyotrophic lateral sclerosis (ALS). A hypothesis as to the nature of SOD1 aggregation implicates oxidative damage to a solvent-exposed tryptophan as causative. Here, we chart discovery of a phenanthridinone based compound (Lig9) from the NCI Diversity Set III by rational methods by in silico screening and crystallographic validation. The crystal structure of the complex with SOD1, refined to 2.5 Å, revealed that Lig9 binds the SOD1 β-barrel in the β-strand 2 and 3 region which is known to scaffold SOD1 fibrillation. The phenanthridinone moiety makes a substantial π - π interaction with Trp32 of SOD1. The compound possesses a significant binding affinity for SOD1 and inhibits oxidation of Trp32; a critical residue for SOD1 aggregation. Thus, Lig9 is a good candidate from which to develop a new library of SOD1 aggregation inhibitors through protection of Trp32 oxidation.


    Organizational Affiliation

    a Department of Biophysics , National Institute of Mental Health and Neurosciences (NIMHANS) , Hosur Road , Bangalore - 560029 , India.,d Neurotoxicology Laboratory , Neurobiology Research Center, National Institute of Mental Health and Neurosciences (NIMHANS) , Hosur Road , Bangalore - 560029 , India.,b Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool , Liverpool L69 7ZB , UK.,c Department of Neurochemistry , National Institute of Mental Health and Neurosciences (NIMHANS) , Hosur Road , Bangalore - 560029 , India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Superoxide dismutase [Cu-Zn]
A, B, C, D, E, F, G, H, I, J
154Homo sapiensMutation(s): 0 
Gene Names: SOD1
EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens)
Go to Gene View: SOD1
Go to UniProtKB:  P00441
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, H, I, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
6B3
Query on 6B3

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Download CCD File 
F
2'-[(6-oxo-5,6-dihydrophenanthridin-3-yl)carbamoyl][1,1'-biphenyl]-2-carboxylic acid
C27 H18 N2 O4
MWPPELUBOBZLKD-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
S4P
Query on S4P

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Download CCD File 
A, C, F
Dihydrogen tetrasulfide
Tetrasulfane
H2 S4
IKRMQEUTISXXQP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 164.367α = 90.00
b = 203.692β = 90.00
c = 144.211γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PHENIXphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-17
    Type: Initial release
  • Version 1.1: 2019-08-14
    Type: Data collection, Database references