4JQH

Crystal structure of a new sGC activator (analogue of BAY 58-2667) bound to nostoc H-NOX domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.132 

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This is version 1.3 of the entry. See complete history. 


Literature

Insights into soluble guanylyl cyclase activation derived from improved heme-mimetics.

von Wantoch Rekowski, M., Kumar, V., Zhou, Z., Moschner, J., Marazioti, A., Bantzi, M., Spyroulias, G.A., van den Akker, F., Giannis, A., Papapetropoulos, A.

(2013) J Med Chem 56: 8948-8952

  • DOI: https://doi.org/10.1021/jm400539d
  • Primary Citation of Related Structures:  
    4JQH

  • PubMed Abstract: 

    Recently, the structure of BAY 58-2667 bound to the Nostoc sp. H-NOX domain was published. On the basis of this structural information, we designed BAY 58-2667 derivatives and tested their effects on soluble guanylyl cyclase (sGC) activity. Derivative 20 activated sGC 4.8-fold more than BAY 58-2667. Co-crystallization of 20 with the Ns H-NOX domain revealed that the increased conformational distortion at the C-terminal region of αF helix containing 110-114 residues contributes to the higher activation triggered by 20.

    • Organizational Affiliation: 

    Institut für Organische Chemie, Universität Leipzig, Leipzig, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alr2278 protein
A, B
189Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 1 
Gene Names: alr2278
EC: 4.6.1.2
UniProt
Find proteins for Q8YUQ7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YUQ7 
Go to UniProtKB:  Q8YUQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YUQ7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.132 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.191α = 90
b = 122.191β = 90
c = 122.191γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-01-15
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations