4A7Q

Structure of human I113T SOD1 mutant complexed with 4-(4-methyl-1,4- diazepan-1-yl)quinazoline in the p21 space group.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-Ray Crystallography and Computational Docking for the Detection and Development of Protein-Ligand Interactions.

Kershaw, N.M.Wright, G.S.Sharma, R.Antonyuk, S.V.Strange, R.W.Berry, N.G.O'Neill, P.M.Hasnain, S.S.

(2013) Curr Med Chem 20: 569

  • DOI: 10.2174/0929867311320040008
  • Primary Citation of Related Structures:  
    4A7G, 4A7Q

  • PubMed Abstract: 
  • Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterised by the selective dysfunction and death of the upper and lower motor neurons. Median survival rates are between 3 and 5 years after diagnosis. Mutations in t ...

    Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterised by the selective dysfunction and death of the upper and lower motor neurons. Median survival rates are between 3 and 5 years after diagnosis. Mutations in the gene encoding Cu/Zn superoxide dismutase (SOD1) have been linked to a subset of familial forms of ALS (fALS). Herein, we describe a fragment- based drug discovery (FBDD) approach for the investigation of small molecule binding sites in SOD1. X-ray crystallography has been used as the primary screening method and has been shown to directly detect protein-ligand interactions which cannot be unambiguously identified using other biophysical methods. The structural requirements for effective binding at Trp32 are detailed for a series of quinazoline-containing compounds. The investigation of an additional site that binds a range of catecholamines and the use of computational modelling to assist fragment evolution is discussed. This study also highlights the importance of ligand solubility for successful Xray crystallographic campaigns in lead compound design.


    Organizational Affiliation

    Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK. nkershaw@liverpool.ac.uk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASE [CU-ZN]AF153Homo sapiensMutation(s): 1 
Gene Names: SOD1
EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
NIH Common Fund Data Resources
PHAROS  P00441
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4MQ
Query on 4MQ

Download CCD File 
A, F
4-(4-METHYL-1,4-DIAZEPAN-1-YL)QUINAZOLINE
C14 H18 N4
BZBWHBGXCGIIRW-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CU
Query on CU

Download CCD File 
A, F
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.22 Å
  • R-Value Free: 0.159 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.01α = 90
b = 68.21β = 104.11
c = 49.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2013-08-28
    Changes: Database references