3L6J

Structure of cinaciguat (bay 58-2667) bound to nostoc H-NOX domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of cinaciguat (BAY 58-2667) bound to Nostoc H-NOX domain reveals insights into heme-mimetic activation of the soluble guanylyl cyclase.

Martin, F.Baskaran, P.Ma, X.Dunten, P.W.Schaefer, M.Stasch, J.P.Beuve, A.van den Akker, F.

(2010) J Biol Chem 285: 22651-22657

  • DOI: https://doi.org/10.1074/jbc.M110.111559
  • Primary Citation of Related Structures:  
    3L6J

  • PubMed Abstract: 

    Heme is a vital molecule for all life forms with heme being capable of assisting in catalysis, binding ligands, and undergoing redox changes. Heme-related dysfunction can lead to cardiovascular diseases with the oxidation of the heme of soluble guanylyl cyclase (sGC) critically implicated in some of these cardiovascular diseases. sGC, the main nitric oxide (NO) receptor, stimulates second messenger cGMP production, whereas reactive oxygen species are known to scavenge NO and oxidize/inactivate the heme leading to sGC degradation. This vulnerability of NO-heme signaling to oxidative stress led to the discovery of an NO-independent activator of sGC, cinaciguat (BAY 58-2667), which is a candidate drug in clinical trials to treat acute decompensated heart failure. Here, we present crystallographic and mutagenesis data that reveal the mode of action of BAY 58-2667. The 2.3-A resolution structure of BAY 58-2667 bound to a heme NO and oxygen binding domain (H-NOX) from Nostoc homologous to that of sGC reveals that the trifurcated BAY 58-2667 molecule has displaced the heme and acts as a heme mimetic. Carboxylate groups of BAY 58-2667 make interactions similar to the heme-propionate groups, whereas its hydrophobic phenyl ring linker folds up within the heme cavity in a planar-like fashion. BAY 58-2667 binding causes a rotation of the alphaF helix away from the heme pocket, as this helix is normally held in place via the inhibitory His(105)-heme covalent bond. The structure provides insights into how BAY 58-2667 binds and activates sGC to rescue heme-NO dysfunction in cardiovascular diseases.


  • Organizational Affiliation

    Department of Biochemistry/RT500, Case Western Reserve University, Cleveland, Ohio 44120, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alr2278 protein
A, B
189Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: alr2278
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Z90
Query on Z90

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
4-({(4-carboxybutyl)[2-(2-{[4-(2-phenylethyl)benzyl]oxy}phenyl)ethyl]amino}methyl)benzoic acid
C36 H39 N O5
WPYWMXNXEZFMAK-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.153 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.268α = 90
b = 123.268β = 90
c = 123.268γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description