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: 2.3 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/jm400539d

  • 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. Derivativ ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alr2278 protein
A, B
189Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)Mutation(s): 1 
Find proteins for Q8YUQ7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Go to UniProtKB:  Q8YUQ7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download SDF File 
Download CCD File 
A, B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
1MF
Query on 1MF

Download SDF File 
Download CCD File 
A, B
4-{[(4-carboxybutyl)(2-{2-[(4'-phenoxybiphenyl-4-yl)methoxy]phenyl}ethyl)amino]methyl}benzoic acid
C40 H39 N O6
KJMQIQGZRNYQSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.129 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 122.191α = 90.00
b = 122.191β = 90.00
c = 122.191γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references
  • Version 1.2: 2015-04-29
    Type: Non-polymer description