9RDU | pdb_00009rdu

Crystal structure of the Protein-Kinase A catalytic subunit from Cricetulus griseus in complex with F001

• PDB DOI: https://doi.org/10.2210/pdb9RDU/pdb

• Classification: TRANSFERASE
• Organism(s): Cricetulus griseus
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2025-06-03 Released: 2025-12-31 
• Deposition Author(s): Mueller, J., Wolter, M., Glinca, S., Klebe, G.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free: 
  0.170 (Depositor), 0.175 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target Exploring Options beyond the Flatland

Santura, A., Muller, J., Wolter, M., Tutzschky, I.C., Ruf, M., Metz, A., Sandner, A., Merkl, S., Klebe, G., Glinca, S., Czodrowski, P.

(2025) J Chem Inf Model 

• DOI: https://doi.org/10.1021/acs.jcim.5c01952

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.17 kDa 
• Atom Count: 3,220 
• Modeled Residue Count: 338 
• Deposited Residue Count: 353 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	353	Cricetulus griseus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P25321 (Cricetulus griseus) Explore P25321  Go to UniProtKB:  P25321

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1JE8 (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	(3~{R},5~{S})-5-[3-(4-fluorophenyl)-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol C12 H12 F N3 O2 FZFUFKCKPSCCJC-ZJUUUORDSA-N
DMS	E [auth A], F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.42 Å
• R-Value Free:  0.170 (Depositor), 0.175 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.535	α = 90
b = 71.709	β = 90
c = 98.695	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-31 
Deposition Author(s): Mueller, J., Wolter, M., Glinca, S., Klebe, G.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-31
  Type: Initial release