6Y2O

Crystal structure of the cAMP-dependent protein kinase A cocrystallized with 1,7-Naphthyridin-8-amine and PKI (5-24)

• PDB DOI: https://doi.org/10.2210/pdb6Y2O/pdb

• Classification: TRANSFERASE
• Organism(s): Cricetulus griseus, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-17 Released: 2020-09-30 
• Deposition Author(s): Oebbeke, M., Heine, A., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.254 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Fragment based drug design - Small chemical changes of fragments effecting big changes in binding

Oebbeke, M., Wienen-Schmidt, B., Gerber, H.-D., Heine, A., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 43.88 kDa 
• Atom Count: 3,081 
• Modelled Residue Count: 371 
• Deposited Residue Count: 373 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B	20	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P63248 (Mus musculus) Explore P63248  Go to UniProtKB:  P63248
IMPC:  MGI:104747

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
O72 (Subject of Investigation/LOI)	H [auth A]	1,7-naphthyridin-8-amine C8 H7 N3 LRKLTZGZHDEBME-UHFFFAOYSA-N
DMS	C [auth A], D [auth A], E [auth A], F [auth A], G [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: 2.01 Å
• R-Value Free: 0.254 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.642	α = 90
b = 74.916	β = 90
c = 106.01	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
Coot	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Oebbeke, M., Heine, A., Klebe, G.

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description