6C0U

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

Summary for 6C0U

• Entry DOI: 10.2210/pdb6c0u/pdb
• Related: 6C0T
• Descriptor: cAMP-dependent protein kinase catalytic subunit alpha, N-[(3R,4R)-4-{[4-(2-fluoro-3-methoxy-6-propoxybenzene-1-carbonyl)benzene-1-carbonyl]amino}pyrrolidin-3-yl]-1H-indazole-5-carboxamide, DIMETHYL SULFOXIDE, ... (5 entities in total)
• Functional Keywords: serine/threonine protein kinase (ec 2.7.11.11), transferase, transferase-transferase inhibitor complex, transferase/transferase inhibitor
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 41979.80

Authors

Qin, L.,Sankaran, B.,Kim, C. (deposition date: 2018-01-02, release date: 2018-05-30, Last modification date: 2024-11-20)

Primary citation

Qin, L.,Sankaran, B.,Aminzai, S.,Casteel, D.E.,Kim, C.
Structural basis for selective inhibition of human PKG I alpha by the balanol-like compound N46.
J. Biol. Chem., 293:10985-10992, 2018

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 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 values for N46, whereas replacing these residues in PKA Cα with those in PKG Iα reduces the IC, 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.

PubMed: 29769318
DOI: 10.1074/jbc.RA118.002427

Experimental method

X-RAY DIFFRACTION (2.65 Å)