Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.10 kDa 
• Atom Count: 2871 
• Residue Count: 306 
• Unique protein chains: 2

4A7G

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

• DOI: 10.2210/pdb4A7G/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-11-14 Released: 2012-10-24 
• Deposition Author(s): Wright, G.S.A., Kershaw, N.M., Sharma, R., Antonyuk, S.V., Strange, R.W., Berry, N.G., O'Neil, P.M., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.175 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 

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: 569-575

• PubMed: 23278398 
• DOI: 10.2174/0929867311320040008
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SUPEROXIDE DISMUTASE [CU-ZN]	A	153	Homo sapiens	Mutation(s): 1  Gene Names: SOD1 EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens) Go to UniProtKB:  P00441
NIH Common Fund Data Resources
PHAROS  P00441 GTEx  ENSG00000142168

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
SUPEROXIDE DISMUTASE [CU-ZN]	F	153	Homo sapiens	Mutation(s): 1  Gene Names: SOD1 EC: 1.15.1.1
Find proteins for P00441 (Homo sapiens) Go to UniProtKB:  P00441
NIH Common Fund Data Resources
PHAROS  P00441 GTEx  ENSG00000142168

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
12I	A, F	4-(4-METHYLPIPERAZIN-1-YL)QUINAZOLINE C13 H16 N4 RDYFSMILBPHDCN-UHFFFAOYSA-N
SO4	A, F	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A, F	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	A, F	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.175 
• R-Value Work: 0.139 
• R-Value Observed: 0.141 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.793	α = 90
b = 68.352	β = 104.49
c = 49.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-14 
• Released Date: 2012-10-24 
Deposition Author(s): Wright, G.S.A., Kershaw, N.M., Sharma, R., Antonyuk, S.V., Strange, R.W., Berry, N.G., O'Neil, P.M., Hasnain, S.S.

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
• Version 1.3: 2018-11-14
  Changes: Data collection, Database references
• Version 1.4: 2018-11-21
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2019-10-09
  Changes: Data collection, Database references, Other