7SSB

Co-structure of PKG1 regulatory domain with compound 33


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

Starting Model: experimental
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Literature

Optimization and Mechanistic Investigations of Novel Allosteric Activators of PKG1 alpha.

Mak, V.W.Patel, A.M.Yen, R.Hanisak, J.Lim, Y.H.Bao, J.Zheng, R.Seganish, W.M.Yu, Y.Healy, D.R.Ogawa, A.Ren, Z.Soriano, A.Ermakov, G.P.Beaumont, M.Metwally, E.Cheng, A.C.Verras, A.Fischmann, T.Zebisch, M.Silvestre, H.L.McEwan, P.A.Barker, J.Rearden, P.Greshock, T.J.

(2022) J Med Chem 65: 10318-10340

  • DOI: https://doi.org/10.1021/acs.jmedchem.1c02109
  • Primary Citation of Related Structures:  
    7SSB

  • PubMed Abstract: 

    Activation of PKG1α is a compelling strategy for the treatment of cardiovascular diseases. As the main effector of cyclic guanosine monophosphate (cGMP), activation of PKG1α induces smooth muscle relaxation in blood vessels, lowers pulmonary blood pressure, prevents platelet aggregation, and protects against cardiac stress. The development of activators has been mostly limited to cGMP mimetics and synthetic peptides. Described herein is the optimization of a piperidine series of small molecules to yield activators that demonstrate in vitro phosphorylation of vasodilator-stimulated phosphoprotein as well as antiproliferative effects in human pulmonary arterial smooth muscle cells. Hydrogen/deuterium exchange mass spectrometry experiments with the small molecule activators revealed a mechanism of action consistent with cGMP-induced activation, and an X-ray co-crystal structure with a construct encompassing the regulatory domains illustrated a binding mode in an allosteric pocket proximal to the low-affinity cyclic nucleotide-binding domain.


  • Organizational Affiliation

    Discovery Chemistry, Merck & Co., Inc., South San Francisco, California 94080, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cGMP-dependent protein kinase 1268Homo sapiensMutation(s): 1 
Gene Names: PRKG1PRKG1BPRKGR1APRKGR1B
EC: 2.7.11.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q13976 (Homo sapiens)
Explore Q13976 
Go to UniProtKB:  Q13976
PHAROS:  Q13976
GTEx:  ENSG00000185532 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13976
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
B4I
Query on B4I

Download Ideal Coordinates CCD File 
B [auth A]4-({(2S,3S)-3-[(1S)-1-(3,5-dichlorophenyl)-2-hydroxyethoxy]-2-phenylpiperidin-1-yl}methyl)-3-nitrobenzoic acid
C27 H26 Cl2 N2 O6
REDPQDQMPNUDEP-NXCFDTQHSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.394α = 90
b = 80.656β = 90
c = 63.222γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-24
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description