6BX6 | pdb_00006bx6

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

• PDB DOI: https://doi.org/10.2210/pdb6BX6/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2017-12-17 Released: 2018-05-09 
• Deposition Author(s): Dite, T.A., Langendorf, C.G., Scott, J.W., Oakhill, J.S.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia), Jack Brockhoff Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.280 (Depositor), 0.319 (DCC) 
• R-Value Work: 
  0.252 (Depositor), 0.289 (DCC) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

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 Biological Chem 293: 8874-8885

• PubMed: 29695504 
• DOI: https://doi.org/10.1074/jbc.RA118.003547
• Primary Citation Related Structures: 
  6BX6


• 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.

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Organizational Affiliation: 
• From the Metabolic Signalling Laboratory and.
Protein Chemistry and Metabolism Unit, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy 3065, Victoria, Australia.
the Prostate Cancer Translational Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia.
the Cancer Program, Biomedicine Discovery Institute, and Department of Anatomy and Developmental Biology, Monash University, Clayton 3800, Victoria, Australia.
the Cell Signalling and Cell Death Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.
the Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria 3010, Australia, and.
the Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria 3000, Australia.
From the Metabolic Signalling Laboratory and [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.07 kDa 
• Atom Count: 1,879 
• Modeled Residue Count: 243 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-2	A	276	Homo sapiens	Mutation(s): 1  Gene Names: PRKAA2, AMPK, AMPK2 EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDJ	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 NEXGBSJERNQRSV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
EDJ	BindingDB:  6BX6	IC50: 108 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.280 (Depositor), 0.319 (DCC) 
• R-Value Work:  0.252 (Depositor), 0.289 (DCC) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.43	α = 90
b = 54.783	β = 96.25
c = 143.188	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Dite, T.A., Langendorf, C.G., Scott, J.W., Oakhill, J.S.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1098459
Jack Brockhoff Foundation	Australia	JBF-4206, 2016

Revision History  

• 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