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 

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Ligand Structure Quality Assessment 


This is version 2.0 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
  • Primary Citation of Related Structures:  
    6B2E, 6B1U

  • 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 type 2 diabetes and insulin resistance ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-2A565Homo 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)
UniProt & NIH Common Fund Data Resources
Find proteins for P54646 (Homo sapiens)
Explore P54646 
Go to UniProtKB:  P54646
PHAROS:  P54646
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit beta-2B272Homo sapiensMutation(s): 0 
Gene Names: PRKAB2
UniProt & NIH Common Fund Data Resources
Find proteins for O43741 (Homo sapiens)
Explore O43741 
Go to UniProtKB:  O43741
PHAROS:  O43741
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit gamma-1C336Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens)
Explore P54619 
Go to UniProtKB:  P54619
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)D7N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G01435GL
GlyCosmos:  G01435GL
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CG7 (Subject of Investigation/LOI)
Query on CG7

Download Ideal Coordinates CCD File 
F [auth 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 (Subject of Investigation/LOI)
Query on STU

Download Ideal Coordinates CCD File 
E [auth A]STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
G [auth C], H [auth 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
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900012
Query on PRD_900012
Dbeta-cyclodextrinOligosaccharide /  Drug delivery Ligand Interaction
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

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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
Australian Research Council (ARC)AustraliaFT130100988
The Marian and EH Flack TrustAustraliaEH Flack Fellowship
Jack Brockhoff FoundationAustraliaJBF 4206, 2016

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary