5EZV

X-ray crystal structure of AMP-activated protein kinase alpha-2/alpha-1 RIM chimaera (alpha-2(1-347)/alpha-1(349-401)/alpha-2(397-end) beta-1 gamma-1) co-crystallized with C2 (5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Structural basis of allosteric and synergistic activation of AMPK by furan-2-phosphonic derivative C2 binding.

Langendorf, C.G., Ngoei, K.R., Scott, J.W., Ling, N.X., Issa, S.M., Gorman, M.A., Parker, M.W., Sakamoto, K., Oakhill, J.S., Kemp, B.E.

(2016) Nat Commun 7: 10912-10912

  • DOI: https://doi.org/10.1038/ncomms10912
  • Primary Citation of Related Structures:  
    4ZHX, 5EZV

  • PubMed Abstract: 

    • The metabolic stress-sensing enzyme AMP-activated protein kinase (AMPK) is responsible for regulating metabolism in response to energy supply and demand. Drugs that activate AMPK may be useful in the treatment of metabolic diseases including type 2 diabetes ...

    The metabolic stress-sensing enzyme AMP-activated protein kinase (AMPK) is responsible for regulating metabolism in response to energy supply and demand. Drugs that activate AMPK may be useful in the treatment of metabolic diseases including type 2 diabetes. We have determined the crystal structure of AMPK in complex with its activator 5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid (C2), revealing two C2-binding sites in the γ-subunit distinct from nucleotide sites. C2 acts synergistically with the drug A769662 to activate AMPK α1-containing complexes independent of upstream kinases. Our results show that dual drug therapies could be effective AMPK-targeting strategies to treat metabolic diseases.

    Organizational Affiliation: 

    Mary MacKillop Institute for Health Research Australian Catholic University, Victoria Parade, Fitzroy, Victoria 3065, Australia.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-2/alpha-1 RIM SWAP chimera
A, C
560Homo sapiensMutation(s): 0 
Gene Names: PRKAA2, AMPK, AMPK2, PRKAA1, AMPK1
EC: 2.7.11.1 (PDB Primary Data), 2.7.11.27 (PDB Primary Data), 2.7.11.31 (PDB Primary Data), 2.7.11.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q13131 (Homo sapiens)
Explore Q13131 
Go to UniProtKB:  Q13131
PHAROS:  Q13131
Find proteins for P54646 (Homo sapiens)
Explore P54646 
Go to UniProtKB:  P54646
PHAROS:  P54646
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ13131P54646
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-1
B, D
270Homo sapiensMutation(s): 0 
Gene Names: PRKAB1, AMPK
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y478 (Homo sapiens)
Explore Q9Y478 
Go to UniProtKB:  Q9Y478
PHAROS:  Q9Y478
Entity Groups  
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UniProt GroupQ9Y478
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-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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54619
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU
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
Query on C1V
Download Ideal Coordinates CCD File 
H [auth A],
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
C2Z
Query on C2Z
Download Ideal Coordinates CCD File 
K [auth E],
L [auth E],
M [auth F],
N [auth F]		5-(5-hydroxyl-isoxazol-3-yl)-furan-2-phosphonic acid
C7 H6 N O6 P
BRLJHMCTDKAUAY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D 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
Binding Affinity Annotations 
IDSourceBinding Affinity
C1V BindingDB:  5EZV Kd: min: 487, max: 1.45e+4 (nM) from 3 assay(s)
EC50: 800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.608α = 90
b = 134.112β = 93.16
c = 141.287γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description