5UZK

Crystal Structure of PKA bound to an pyrrolo pyridine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5UZK/pdb

• Classification: Transferase/Transferase Inhibitor
• Organism(s): Homo sapiens, Oryctolagus cuniculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-26 Released: 2018-03-07 
• Deposition Author(s): Jacobs, M.D., Brown, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

ROCK inhibitors 3: Design, synthesis and structure-activity relationships of 7-azaindole-based Rho kinase (ROCK) inhibitors.

Bandarage, U.K., Cao, J., Come, J.H., Court, J.J., Gao, H., Jacobs, M.D., Marhefka, C., Nanthakumar, S., Green, J.

(2018) Bioorg Med Chem Lett 28: 2622-2626

• PubMed: 30082069 
• DOI: https://doi.org/10.1016/j.bmcl.2018.06.040
• Primary Citation of Related Structures:  
  5UZJ, 5UZK


• PubMed Abstract: 
  

  Rho kinase (ROCK) inhibitors are potential therapeutic agents for the treatment of a variety of disorders including hypertension, glaucoma and erectile dysfunction. Here we disclose a series of potent and selective ROCK inhibitors based on a substituted 7-azaindole scaffold. Substitution of the 3-position of 7-azaindole led to compounds such as 37, which possess excellent ROCK inhibitory potency and high selectivity against the closely related kinase PKA.

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Organizational Affiliation: 

Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, MA 02210, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 43.26 kDa 
• Atom Count: 3,195 
• Modelled Residue Count: 355 
• Deposited Residue Count: 369 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase catalytic subunit alpha	A	351	Homo sapiens	Mutation(s): 0  Gene Names: PRKACA, PKACA EC: 2.7.11.11
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612  Go to UniProtKB:  P17612
PHAROS:  P17612 GTEx:  ENSG00000072062

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase inhibitor alpha	B [auth I]	18	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P61926 (Oryctolagus cuniculus) Explore P61926  Go to UniProtKB:  P61926

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
504	C [auth A]	2-{3-[3-(piperidin-4-yl)propoxy]phenyl}-N-[4-(1H-pyrrolo[2,3-b]pyridin-3-yl)-1,3-thiazol-2-yl]acetamide C26 H29 N5 O2 S OKUPZBPYLVKVSU-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

Binding Affinity Annotations
ID	Source	Binding Affinity
504	Binding MOAD:  5UZK	Ki: 180 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.253 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.17	α = 90
b = 78.18	β = 90
c = 80.26	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-03-07 
Deposition Author(s): Jacobs, M.D., Brown, K.

Revision History  

• Version 1.0: 2018-03-07
  Type: Initial release
  
• Version 1.1: 2018-07-11
  Changes: Data collection, Database references
• Version 1.2: 2018-08-22
  Changes: Data collection, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description