6B2E

Structure of full length human AMPK (a2b2g1) in complex with a small molecule activator SC4.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Determinants for Small-Molecule Activation of Skeletal Muscle AMPK alpha 2 beta 2 gamma 1 by the Glucose Importagog SC4.

Ngoei, K.R.W.Langendorf, C.G.Ling, N.X.Y.Hoque, A.Varghese, S.Camerino, M.A.Walker, S.R.Bozikis, Y.E.Dite, T.A.Ovens, A.J.Smiles, W.J.Jacobs, R.Huang, H.Parker, M.W.Scott, J.W.Rider, M.H.Foitzik, R.C.Kemp, B.E.Baell, J.B.Oakhill, J.S.

(2018) Cell Chem Biol 25: 728-737.e9

  • DOI: 10.1016/j.chembiol.2018.03.008
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The AMP-activated protein kinase (AMPK) αβγ heterotrimer regulates cellular energy homeostasis with tissue-specific isoform distribution. Small-molecule activation of skeletal muscle α2β2 AMPK complexes may prove a valuable treatment strategy for typ ...

    The AMP-activated protein kinase (AMPK) αβγ heterotrimer regulates cellular energy homeostasis with tissue-specific isoform distribution. Small-molecule activation of skeletal muscle α2β2 AMPK complexes may prove a valuable treatment strategy for type 2 diabetes and insulin resistance. Herein, we report the small-molecule SC4 is a potent, direct AMPK activator that preferentially activates α2 complexes and stimulates skeletal muscle glucose uptake. In parallel with the term secretagog, we propose "importagog" to define a substance that induces or augments cellular uptake of another substance. Three-dimensional structures of the glucose importagog SC4 bound to activated α2β2γ1 and α2β1γ1 complexes reveal binding determinants, in particular a key interaction between the SC4 imidazopyridine 4'-nitrogen and β2-Asp111, which provide a design paradigm for β2-AMPK therapeutics. The α2β2γ1/SC4 structure reveals an interaction between a β2 N-terminal α helix and the α2 autoinhibitory domain. Our results provide a structure-function guide to accelerate development of potent, but importantly tissue-specific, β2-AMPK therapeutics.


    Organizational Affiliation

    Metabolic Signalling Laboratory, St. Vincent's Institute of Medical Research, University of Melbourne, Fitzroy, VIC 3065, Australia; Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, VIC 3000, Australia. Electronic address: joakhill@svi.edu.au.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-2
A
565Homo sapiensMutation(s): 0 
Gene Names: PRKAA2AMPKAMPK2
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data)
Find proteins for P54646 (Homo sapiens)
Go to UniProtKB:  P54646
NIH Common Fund Data Resources
PHAROS  P54646

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-2
B
272Homo sapiensMutation(s): 0 
Gene Names: PRKAB2
Find proteins for O43741 (Homo sapiens)
Go to UniProtKB:  O43741
NIH Common Fund Data Resources
PHAROS  O43741

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1
C
336Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
Find proteins for P54619 (Homo sapiens)
Go to UniProtKB:  P54619
NIH Common Fund Data Resources
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCD
Query on BCD

Download CCD File 
B
BETA-CYCLODEXTRIN
C42 H70 O35
WHGYBXFWUBPSRW-FOUAGVGXSA-N
 Ligand Interaction
CG7
Query on CG7

Download CCD File 
A
5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-imidazo[4,5-b]pyridin-2-yl]oxy}-2-methylbenzoic acid
C26 H18 Cl N3 O4
MEZQZPGDJJEQPZ-UHFFFAOYSA-N
 Ligand Interaction
STU
Query on STU

Download CCD File 
A
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
AMP
Query on AMP

Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.936α = 90
b = 118.848β = 90
c = 138.096γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1098459
Australian Research Council (ARC)AustraliaFT130100988
The Marian and EH Flack TrustAustraliaEH Flack Fellowship
Jack Brockhoff FoundationAustraliaJBF 4206, 2016

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-07-04
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence