4A7G

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

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 

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This is version 1.5 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: 569-575

  • 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 the gene encoding Cu/Zn superoxide dismutase (SOD1) have been linked to a subset of familial forms of ALS (fALS) ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASE [CU-ZN]A153Homo 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
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUPEROXIDE DISMUTASE [CU-ZN]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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
12I
Query on 12I
Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
O [auth F]		4-(4-METHYLPIPERAZIN-1-YL)QUINAZOLINE
C13 H16 N4
RDYFSMILBPHDCN-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
E [auth A],
J [auth F],
K [auth F],
M [auth F]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
H [auth A],
N [auth F]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CU
Query on CU
Download Ideal Coordinates CCD File 
G [auth A],
L [auth F]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
I [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
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 = 38.793α = 90
b = 68.352β = 104.49
c = 49.92γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

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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
  • 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