6E4W

Structure of AMPK bound to activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Acyl Glucuronide Metabolites of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1 H-indole-3-carboxylic Acid (PF-06409577) and Related Indole-3-carboxylic Acid Derivatives are Direct Activators of Adenosine Monophosphate-Activated Protein Kinase (AMPK).

Ryder, T.F.Calabrese, M.F.Walker, G.S.Cameron, K.O.Reyes, A.R.Borzilleri, K.A.Delmore, J.Miller, R.Kurumbail, R.G.Ward, J.Kung, D.W.Brown, J.A.Edmonds, D.J.Eng, H.Wolford, A.C.Kalgutkar, A.S.

(2018) J Med Chem 61: 7273-7288

  • DOI: 10.1021/acs.jmedchem.8b00807
  • Primary Citation of Related Structures:  
    6E4U, 6E4W, 6E4T

  • PubMed Abstract: 
  • Studies on indole-3-carboxylic acid derivatives as direct activators of human adenosine monophosphate-activated protein kinase (AMPK) α1β1γ1 isoform have culminated in the identification of PF-06409577 (1), PF-06885249 (2), and PF-06679142 (3) as pot ...

    Studies on indole-3-carboxylic acid derivatives as direct activators of human adenosine monophosphate-activated protein kinase (AMPK) α1β1γ1 isoform have culminated in the identification of PF-06409577 (1), PF-06885249 (2), and PF-06679142 (3) as potential clinical candidates. Compounds 1-3 are primarily cleared in animals and humans via glucuronidation. Herein, we describe the biosynthetic preparation, purification, and structural characterization of the glucuronide conjugates of 1-3. Spectral characterization of the purified glucuronides M1, M2, and M3 indicated that they were acyl glucuronide derivatives. In vitro pharmacological evaluation revealed that all three acyl glucuronides retained selective activation of β1-containing AMPK isoforms. Inhibition of de novo lipogenesis with representative parent carboxylic acids and their respective acyl glucuronide conjugates in human hepatocytes demonstrated their propensity to activate cellular AMPK. Cocrystallization of the AMPK α1β1γ1 isoform with 1-3 and M1-M3 provided molecular insights into the structural basis for AMPK activation by the glucuronide conjugates.


    Organizational Affiliation

    Medicine Design , Pfizer Worldwide Research & Development , Groton , Connecticut 06340 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit gamma-1C330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus)
Explore P80385 
Go to UniProtKB:  P80385
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase catalytic subunit alpha-1A503Rattus norvegicusMutation(s): 0 
Gene Names: Prkaa1Ampk1
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 (PDB Primary Data)
Find proteins for P54645 (Rattus norvegicus)
Explore P54645 
Go to UniProtKB:  P54645
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
5'-AMP-activated protein kinase subunit beta-1B204Rattus norvegicusMutation(s): 0 
Gene Names: Prkab1
Find proteins for P80386 (Rattus norvegicus)
Explore P80386 
Go to UniProtKB:  P80386
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HUG
Query on HUG

Download CCD File 
A
1-O-(4,6-difluoro-5-{4-[(2S)-oxan-2-yl]phenyl}-1H-indole-3-carbonyl)-beta-D-glucopyranuronic acid
C26 H25 F2 N O9
GZCJKJJWOUAGMR-WBTGXFMPSA-N
 Ligand Interaction
STU
Query on STU

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A
STAUROSPORINE
C28 H26 N4 O3
HKSZLNNOFSGOKW-FYTWVXJKSA-N
 Ligand Interaction
ADP
Query on ADP

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C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP
Query on AMP

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C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

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C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.210 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.97α = 90
b = 123.97β = 90
c = 402.12γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
autoXDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-09-05
    Changes: Data collection, Database references