5KQ5

AMPK bound to allosteric activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and Preclinical Characterization of 6-Chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1H-indole-3-carboxylic Acid (PF-06409577), a Direct Activator of Adenosine Monophosphate-activated Protein Kinase (AMPK), for the Potential Treatment of Diabetic Nephropathy.

Cameron, K.O.Kung, D.W.Kalgutkar, A.S.Kurumbail, R.G.Miller, R.Salatto, C.T.Ward, J.Withka, J.M.Bhattacharya, S.K.Boehm, M.Borzilleri, K.A.Brown, J.A.Calabrese, M.Caspers, N.L.Cokorinos, E.Conn, E.L.Dowling, M.S.Edmonds, D.J.Eng, H.Fernando, D.P.Frisbie, R.Hepworth, D.Landro, J.Mao, Y.Rajamohan, F.Reyes, A.R.Rose, C.R.Ryder, T.Shavnya, A.Smith, A.C.Tu, M.Wolford, A.C.Xiao, J.

(2016) J Med Chem 59: 8068-8081

  • DOI: 10.1021/acs.jmedchem.6b00866
  • Primary Citation of Related Structures:  
    5KQ5

  • PubMed Abstract: 
  • Adenosine monophosphate-activated protein kinase (AMPK) is a protein kinase involved in maintaining energy homeostasis within cells. On the basis of human genetic association data, AMPK activators were pursued for the treatment of diabetic nephropathy. Identification of an indazole amide high throughput screening (HTS) hit followed by truncation to its minimal pharmacophore provided an indazole acid lead compound ...

    Adenosine monophosphate-activated protein kinase (AMPK) is a protein kinase involved in maintaining energy homeostasis within cells. On the basis of human genetic association data, AMPK activators were pursued for the treatment of diabetic nephropathy. Identification of an indazole amide high throughput screening (HTS) hit followed by truncation to its minimal pharmacophore provided an indazole acid lead compound. Optimization of the core and aryl appendage improved oral absorption and culminated in the identification of indole acid, PF-06409577 (7). Compound 7 was advanced to first-in-human trials for the treatment of diabetic nephropathy.


    Organizational Affiliation

    Cardiovascular, Metabolic and Endocrine Diseases Medicinal Chemistry, ⊥Cardiovascular, Metabolic and Endocrine Diseases Research Unit, #Worldwide Medicinal Chemistry, ∇Pharmacokinetics, Dynamics and Metabolism, ○Pharmaceutical Sciences, Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
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)
UniProt
Find proteins for P54645 (Rattus norvegicus)
Explore P54645 
Go to UniProtKB:  P54645
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-1B204Rattus norvegicusMutation(s): 1 
Gene Names: Prkab1
UniProt
Find proteins for P80386 (Rattus norvegicus)
Explore P80386 
Go to UniProtKB:  P80386
Protein Feature View
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  • Reference Sequence
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
UniProt
Find proteins for P80385 (Rattus norvegicus)
Explore P80385 
Go to UniProtKB:  P80385
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STU (Subject of Investigation/LOI)
Query on STU

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

Download Ideal Coordinates CCD File 
L [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
J [auth C], K [auth C]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
6VT (Subject of Investigation/LOI)
Query on 6VT

Download Ideal Coordinates CCD File 
E [auth A]6-chloranyl-5-[4-(1-oxidanylcyclobutyl)phenyl]-1~{H}-indole-3-carboxylic acid
C19 H16 Cl N O3
FHQXLWCFSUSXBF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
M [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], H [auth A], I [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
6VT BindingDB:  5KQ5 Kd: 9 (nM) from 1 assay(s)
IC50: 400 (nM) from 1 assay(s)
EC50: min: 1.9, max: 28 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.41 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.5α = 90
b = 124.5β = 90
c = 402.25γ = 120
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations