9IC2 | pdb_00009ic2

Structure of AMPK-alpha2-kinase domain bound to BAY-3827

• PDB DOI: https://doi.org/10.2210/pdb9IC2/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-14 Released: 2025-09-03 
• Deposition Author(s): Ahangar, M.S., Zeqiraj, E., Fraguas Bringas, C., Sakamoto, K.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structure of AMPK-alpha2-kinase domain bound to BAY-3827

Ahangar, M.S., Zeqiraj, E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.22 kDa 
• Atom Count: 2,230 
• Modeled Residue Count: 267 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-AMP-activated protein kinase catalytic subunit alpha-2	A	276	Homo sapiens	Mutation(s): 0  Gene Names: PRKAA2, AMPK, AMPK2 EC: 2.7.11.1 (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 GTEx:  ENSG00000162409

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1I1Y (Subject of Investigation/LOI)	B [auth A]	~{N}-[5-(3,5-dicyano-1,2,6-trimethyl-4~{H}-pyridin-4-yl)-6-fluoranyl-7-methyl-1~{H}-indazol-3-yl]-2-ethyl-benzamide C27 H25 F N6 O OZFFKOSQNBBYCA-UHFFFAOYSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.235 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.176	α = 90
b = 117.778	β = 90
c = 38.327	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Ahangar, M.S., Zeqiraj, E., Fraguas Bringas, C., Sakamoto, K.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release