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 

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Ligand Structure Quality Assessment 


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: https://doi.org/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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASE [CU-ZN]A,
B [auth F]
153Homo sapiensMutation(s): 1 
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
4MQ
Query on 4MQ

Download Ideal Coordinates CCD File 
C [auth A],
I [auth F]
4-(4-METHYL-1,4-DIAZEPAN-1-YL)QUINAZOLINE
C14 H18 N4
BZBWHBGXCGIIRW-UHFFFAOYSA-N
SO4
Query on SO4

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

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

Download Ideal Coordinates CCD File 
G [auth A],
L [auth F]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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