7MYJ

Structure of full length human AMPK (a2b1g1) in complex with a small molecule activator MSG011


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-function analysis of the AMPK activator SC4 and identification of a potent pan AMPK activator.

Ovens, A.J.Gee, Y.S.Ling, N.X.Y.Yu, D.Hardee, J.P.Chung, J.D.Ngoei, K.R.W.Waters, N.J.Hoffman, N.J.Scott, J.W.Loh, K.Spengler, K.Heller, R.Parker, M.W.Lynch, G.S.Huang, F.Galic, S.Kemp, B.E.Baell, J.B.Oakhill, J.S.Langendorf, C.G.

(2022) Biochem J 479: 1181-1204

  • DOI: https://doi.org/10.1042/BCJ20220067
  • Primary Citation of Related Structures:  
    7MYJ

  • PubMed Abstract: 

    The AMP-activated protein kinase (AMPK) αβγ heterotrimer is a primary cellular energy sensor and central regulator of energy homeostasis. Activating skeletal muscle AMPK with small molecule drugs improves glucose uptake and provides an opportunity for new strategies to treat type 2 diabetes and insulin resistance, with recent genetic and pharmacological studies indicating the α2β2γ1 isoform combination as the heterotrimer complex primarily responsible. With the goal of developing α2β2-specific activators, here we perform structure/function analysis of the 2-hydroxybiphenyl group of SC4, an activator with tendency for α2-selectivity that is also capable of potently activating β2 complexes. Substitution of the LHS 2-hydroxyphenyl group with polar-substituted cyclohexene-based probes resulted in two AMPK agonists, MSG010 and MSG011, which did not display α2-selectivity when screened against a panel of AMPK complexes. By radiolabel kinase assay, MSG010 and MSG011 activated α2β2γ1 AMPK with one order of magnitude greater potency than the pan AMPK activator MK-8722. A crystal structure of MSG011 complexed to AMPK α2β1γ1 revealed a similar binding mode to SC4 and the potential importance of an interaction between the SC4 2-hydroxyl group and α2-Lys31 for directing α2-selectivity. MSG011 induced robust AMPK signalling in mouse primary hepatocytes and commonly used cell lines, and in most cases this occurred in the absence of changes in phosphorylation of the kinase activation loop residue α-Thr172, a classical marker of AMP-induced AMPK activity. These findings will guide future design of α2β2-selective AMPK activators, that we hypothesise may avoid off-target complications associated with indiscriminate activation of AMPK throughout the body.


  • Organizational Affiliation

    Metabolic Signalling Laboratory, St. Vincent's Institute of Medical Research, Fitzroy 3065, Australia.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-2
A, C
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)
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
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit beta-1
B, D
270Homo sapiensMutation(s): 0 
Gene Names: PRKAB1AMPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens)
Explore Q9Y478 
Go to UniProtKB:  Q9Y478
PHAROS:  Q9Y478
GTEx:  ENSG00000111725 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y478
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit gamma-1
E, F
336Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
UniProt & NIH Common Fund Data Resources
Find proteins for P54619 (Homo sapiens)
Explore P54619 
Go to UniProtKB:  P54619
PHAROS:  P54619
GTEx:  ENSG00000181929 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54619
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZQV (Subject of Investigation/LOI)
Query on ZQV

Download Ideal Coordinates CCD File 
H [auth A],
J [auth D]
5-({5-[(4'R)-4'-acetamido-2',3',4',5'-tetrahydro[1,1'-biphenyl]-4-yl]-6-chloro-1H-imidazo[4,5-b]pyridin-2-yl}oxy)-2-methylbenzoic acid
C28 H25 Cl N4 O4
DYYYOJWTTPYOIK-FQEVSTJZSA-N
4O7
Query on 4O7

Download Ideal Coordinates CCD File 
G [auth A],
I [auth C]
(5S,6R,7R,9R,13cR,14R,16aS)-6-methoxy-5-methyl-7-(methylamino)-6,7,8,9,14,15,16,16a-octahydro-5H,13cH-5,9-epoxy-4b,9a,1 5-triazadibenzo[b,h]cyclonona[1,2,3,4-jkl]cyclopenta[e]-as-indacen-14-ol
C28 H30 N4 O3
FJJCTPAMIAOFJX-VWKRKTLRSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
K [auth E],
L [auth E],
M [auth F],
N [auth F]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
B, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.844α = 90
b = 134.199β = 92.55
c = 141.821γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Cootmodel building
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)AustraliaGNT1143080
National Health and Medical Research Council (NHMRC, Australia)Australia1098459
National Health and Medical Research Council (NHMRC, Australia)Australia1145265
National Health and Medical Research Council (NHMRC, Australia)Australia1138102
Australian Research Council (ARC)AustraliaDP170101196

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description