6E4T

Structure of AMPK bound to activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.216 

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase catalytic subunit alpha-1
A
503Rattus norvegicusMutation(s): 0 
Gene Names: Prkaa1 (Ampk1)
EC: 2.7.11.1
Find proteins for P54645 (Rattus norvegicus)
Go to UniProtKB:  P54645
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit beta-1
B
204Rattus norvegicusMutation(s): 0 
Gene Names: Prkab1
Find proteins for P80386 (Rattus norvegicus)
Go to UniProtKB:  P80386
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
5'-AMP-activated protein kinase subunit gamma-1
C
330Rattus norvegicusMutation(s): 0 
Gene Names: Prkag1
Find proteins for P80385 (Rattus norvegicus)
Go to UniProtKB:  P80385
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
STU
Query on STU

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

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Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
HTV
Query on HTV

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Download CCD File 
A
1-O-{6-chloro-5-[4-(1-hydroxycyclobutyl)phenyl]-1H-indole-3-carbonyl}-beta-D-glucopyranuronic acid
C25 H24 Cl N O9
LTLTUJCGZGVBTO-DCIKREJASA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.216 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 123.610α = 90.00
b = 123.610β = 90.00
c = 402.550γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
autoXDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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