6C0U

Crystal structure of cAMP-dependent protein kinase Calpha subunit bound with N46


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 protein kinase G (PKG) Iα in nociceptive neurons induces 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 selec ...

    Activation of protein kinase G (PKG) Iα in nociceptive neurons induces 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 attenuate 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. Phe-371 at the PKG Iα glycine-rich loop is oriented parallel to the phenyl ring of N46, forming a strong π-stacking interaction, whereas the analogous Phe-54 in PKA Cα rotates 30° and forms a weaker interaction. Structural comparison revealed that steric hindrance between the preceding Ser-53 and the propoxy group of the phenyl ring may explain the weaker interaction with PKA Cα. The analogous Gly-370 in PKG Iα, however, causes little steric hindrance with Phe-371. Moreover, Ile-406 on the αC helix forms a hydrophobic interaction with N46 whereas its counterpart in PKA, Thr-88, does not. Substituting these residues in PKG Iα with those in PKA Cα increases the IC 50 values for N46, whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC 50 , 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

    From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030.,From the Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, ckim@bcm.edu.,the Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas 77030.,the Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,the Department of Medicine, University of California, San Diego, La Jolla, California 92093, and.,the Department of Medicine, University of California, San Diego, La Jolla, California 92093, and dcasteel@ucsd.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase catalytic subunit alpha
A
354Homo sapiensMutation(s): 0 
Gene Names: PRKACA (PKACA)
EC: 2.7.11.11
Find proteins for P17612 (Homo sapiens)
Go to Gene View: PRKACA
Go to UniProtKB:  P17612
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
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 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  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.208 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 120.494α = 90.00
b = 120.494β = 90.00
c = 80.810γ = 120.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
PHENIXphasing
PHENIXrefinement
Aimlessdata scaling

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
  • Version 1.2: 2019-02-20
    Type: Author supporting evidence, Data collection