AMP-Activated protein kinase (AMPK) inhibition by SBI-0206965: alpha 2 kinase domain bound to SBI-0206965

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 

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AMP-activated protein kinase selectively inhibited by the type II inhibitor SBI-0206965.

Dite, T.A.Langendorf, C.G.Hoque, A.Galic, S.Rebello, R.J.Ovens, A.J.Lindqvist, L.M.Ngoei, K.R.W.Ling, N.X.Y.Furic, L.Kemp, B.E.Scott, J.W.Oakhill, J.S.

(2018) J Biol Chem 293: 8874-8885

  • DOI: https://doi.org/10.1074/jbc.RA118.003547
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Inhibition of the metabolic regulator AMP-activated protein kinase (AMPK) is increasingly being investigated for its therapeutic potential in diseases where AMPK hyperactivity results in poor prognoses, as in established cancers and neurodegeneration. However, AMPK-inhibitory tool compounds are largely limited to compound C, which has a poor selectivity profile. Here we identify the pyrimidine derivative SBI-0206965 as a direct AMPK inhibitor. SBI-0206965 inhibits AMPK with 40-fold greater potency and markedly lower kinase promiscuity than compound C and inhibits cellular AMPK signaling. Biochemical characterization reveals that SBI-0206965 is a mixed-type inhibitor. A co-crystal structure of the AMPK kinase domain/SBI-0206965 complex shows that the drug occupies a pocket that partially overlaps the ATP active site in a type IIb inhibitor manner. SBI-0206965 has utility as a tool compound for investigating physiological roles for AMPK and provides fresh impetus to small-molecule AMPK inhibitor therapeutic development.

  • Organizational Affiliation

    the Cancer Program, Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-2276Homo sapiensMutation(s): 1 
EC: (PDB Primary Data), (PDB Primary Data), (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P54646 (Homo sapiens)
Explore P54646 
Go to UniProtKB:  P54646
PHAROS:  P54646
GTEx:  ENSG00000162409 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54646
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDJ

Download Ideal Coordinates CCD File 
B [auth A]2-({5-bromo-2-[(3,4,5-trimethoxyphenyl)amino]pyrimidin-4-yl}oxy)-N-methylbenzene-1-carboximidic acid
C21 H21 Br N4 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.253 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.43α = 90
b = 54.783β = 96.25
c = 143.188γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1098459
Jack Brockhoff FoundationAustraliaJBF-4206, 2016

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-20
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description