6C0T

Crystal structure of cGMP-dependent protein kinase Ialpha (PKG Ialpha) catalytic domain bound with N46


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for selective inhibition of human PKG I alpha by the balanol-like compound N46.

Qin, L.Sankaran, B.Aminzai, S.Casteel, D.E.Kim, C.

(2018) J. Biol. Chem. 293: 10985-10992

  • DOI: 10.1074/jbc.RA118.002427
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Activation of PKG Iα in nociceptive neurons induces a long-term hyperexcitability that causes chronic pain. Recently, a derivative of the fungal metabolite balanol, N46, has been reported to inhibit PKG Iα with high potency and selectivity and attenu ...

    Activation of PKG Iα in nociceptive neurons induces a long-term hyperexcitability that causes chronic pain. Recently, a derivative of the fungal metabolite balanol, N46, has been reported to inhibit PKG Iα with high potency and selectivity and attenuates thermal hyperalgesia and osteoarthritic pain. Here, we determined co-crystal structures of the PKG Iα C-domain and cAMP-dependent protein kinase (PKA) Cα, each bound with N46, at 1.98 Å and 2.65 Å, respectively. N46 binds the active site with its external phenyl ring specifically interacting with the glycine-rich loop and the αC helix. Phe371 at the PKG Iα glycine-rich loop is oriented parallel to the phenyl ring of N46, forming a strong π-stacking interaction, while the analogous Phe54 in PKA Cα rotates 30º and forms a weaker interaction. Structural comparison revealed that steric hindrance between the preceding Ser53 and the propoxy group of the phenyl ring may explain the weaker interaction with PKA Cα. The analogous Gly370 in PKG Iα, however, causes little steric hindrance with Phe371. Moreover, Ile406 on the αC helix forms a hydrophobic interaction with N46 while its counterpart in PKA, Thr88, does not. Substituting these residues in PKG Iα with those in PKA Cα increases its IC50 values for N46 whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC50, consistent with our structural findings. In conclusion, our results explain the structural basis for N46-mediated selective inhibition of human PKG Iα and provide a starting point for structure-guided design of selective PKG Iα inhibitors.


    Organizational Affiliation

    Baylor College of Medicine, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cGMP-dependent protein kinase 1
A
347Homo sapiensMutation(s): 0 
Gene Names: PRKG1 (PRKG1B, PRKGR1A, PRKGR1B)
EC: 2.7.11.12
Find proteins for Q13976 (Homo sapiens)
Go to Gene View: PRKG1
Go to UniProtKB:  Q13976
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EE4
Query on EE4

Download SDF File 
Download CCD File 
A
N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide
C30 H30 F N5 O5
AYXNTJKOINXKAJ-DHIUTWEWSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.207 
  • Space Group: P 42
Unit Cell:
Length (Å)Angle (°)
a = 85.730α = 90.00
b = 85.730β = 90.00
c = 50.664γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
Aimlessdata scaling
iMOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5R01GM090161-08

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references