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: 3.92 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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:  
    4CFE, 4CFF

  • 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 either AMP or ADP promotes and maintains the phosphorylation of threonine 172 within the activation loop of the kinase ...

    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

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-2A, C571Homo 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-1B, D286Homo 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
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-1E, F331Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU (Subject of Investigation/LOI)
Query on STU

Download Ideal Coordinates CCD File 
G [auth A], I [auth C]STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
C1V (Subject of Investigation/LOI)
Query on C1V

Download Ideal Coordinates CCD File 
H [auth B], J [auth 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
AMP (Subject of Investigation/LOI)
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
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, CL-PEPTIDE LINKINGC4 H10 N O6 PTHR
SEP
Query on SEP
B, DL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
C1V BindingDB:  4CFF Kd: min: 487, max: 1.45e+4 (nM) from 3 assay(s)
EC50: 800 (nM) from 1 assay(s)
PDBBind:  4CFF Kd: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.92 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.019α = 90
b = 134.787β = 93.04
c = 141.286γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-25
    Type: Initial release
  • Version 1.1: 2014-01-08
    Changes: Database references
  • Version 1.2: 2014-02-12
    Changes: Data collection, Other, Refinement description
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other