4CFF

Structure of full length human AMPK in complex with a small molecule activator, a thienopyridone derivative (A-769662)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.924 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis of Ampk Regulation by Small Molecule Activators.

Xiao, B.Sanders, M.J.Carmena, D.Bright, N.J.Haire, L.F.Underwood, E.Patel, B.R.Heath, R.B.Walker, P.A.Hallen, S.Giordanetto, F.Martin, S.R.Carling, D.Gamblin, S.J.

(2013) Nat.Commun. 4: 3017

  • DOI: 10.1038/ncomms4017
  • Primary Citation of Related Structures:  
  • Also Cited By: 4CFH

  • PubMed Abstract: 
  • AMP-activated protein kinase (AMPK) plays a major role in regulating cellular energy balance by sensing and responding to increases in AMP/ADP concentration relative to ATP. Binding of AMP causes allosteric activation of the enzyme and binding of eit ...

    AMP-activated protein kinase (AMPK) plays a major role in regulating cellular energy balance by sensing and responding to increases in AMP/ADP concentration relative to ATP. Binding of AMP causes allosteric activation of the enzyme and binding of either AMP or ADP promotes and maintains the phosphorylation of threonine 172 within the activation loop of the kinase. AMPK has attracted widespread interest as a potential therapeutic target for metabolic diseases including type 2 diabetes and, more recently, cancer. A number of direct AMPK activators have been reported as having beneficial effects in treating metabolic diseases, but there has been no structural basis for activator binding to AMPK. Here we present the crystal structure of human AMPK in complex with a small molecule activator that binds at a site between the kinase domain and the carbohydrate-binding module, stabilising the interaction between these two components. The nature of the activator-binding pocket suggests the involvement of an additional, as yet unidentified, metabolite in the physiological regulation of AMPK. Importantly, the structure offers new opportunities for the design of small molecule activators of AMPK for treatment of metabolic disorders.


    Organizational Affiliation

    1] MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2
A, C
571Homo sapiensMutation(s): 0 
Gene Names: PRKAA2 (AMPK, AMPK2)
EC: 2.7.11.1
Find proteins for P54646 (Homo sapiens)
Go to Gene View: PRKAA2
Go to UniProtKB:  P54646
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
B, D
286Homo sapiensMutation(s): 0 
Gene Names: PRKAB1 (AMPK)
Find proteins for Q9Y478 (Homo sapiens)
Go to Gene View: PRKAB1
Go to UniProtKB:  Q9Y478
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
E, F
331Homo sapiensMutation(s): 0 
Gene Names: PRKAG1
Find proteins for P54619 (Homo sapiens)
Go to Gene View: PRKAG1
Go to UniProtKB:  P54619
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C1V
Query on C1V

Download SDF File 
Download CCD File 
B, C
3-[4-(2-hydroxyphenyl)phenyl]-4-oxidanyl-6-oxidanylidene-7H-thieno[2,3-b]pyridine-5-carbonitrile
C20 H12 N2 O3 S
CTESJDQKVOEUOY-UHFFFAOYSA-N
 Ligand Interaction
STU
Query on STU

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

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Download CCD File 
E, F
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B, D
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, C
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C1VKd: 400 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.924 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 76.019α = 90.00
b = 134.787β = 93.04
c = 141.286γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-08
    Type: Database references
  • Version 1.2: 2014-02-12
    Type: Data collection, Other, Refinement description