5VIB | pdb_00005vib

Crystal structure of Protein Kinase A in complex with the PKI peptide and Aminobenzothiazole based inhibitors

• PDB DOI: https://doi.org/10.2210/pdb5VIB/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-14 Released: 2018-01-31 
• Deposition Author(s): Judge, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Literature

Design of Aminobenzothiazole Inhibitors of Rho Kinases 1 and 2 by Using Protein Kinase A as a Structure Surrogate.

Judge, R.A., Vasudevan, A., Scott, V.E., Simler, G.H., Pratt, S.D., Namovic, M.T., Putman, C.B., Aguirre, A., Stoll, V.S., Mamo, M., Swann, S.I., Cassar, S.C., Faltynek, C.R., Kage, K.L., Boyce-Rustay, J.M., Hobson, A.D.

(2018) Chembiochem 19: 613-621

• PubMed: 29314498 
• DOI: https://doi.org/10.1002/cbic.201700547
• Primary Citation Related Structures: 
  5VHB, 5VI9, 5VIB


• PubMed Abstract: 
  

  We describe the design, synthesis, and structure-activity relationships (SARs) of a series of 2-aminobenzothiazole inhibitors of Rho kinases (ROCKs) 1 and 2, which were optimized to low nanomolar potencies by use of protein kinase A (PKA) as a structure surrogate to guide compound design. A subset of these molecules also showed robust activity in a cell-based myosin phosphatase assay and in a mechanical hyperalgesia in vivo pain model.

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Organizational Affiliation: 
• AbbVie, Inc., 1 North Waukegan Road, North Chicago, IL, 60064, USA.
AbbVie Bioresearch Center, 100 Research Drive, Worcester, MA, 01605, USA.
Current address: Novartis Institute for Biomedical Research, 4560 Horton Street, Emeryville, CA, 94608, USA.
Current address: Takeda Pharmaceuticals, 10410 Science Center Drive, San Diego, CA, 92121, USA.
Current address: Altor Bioscience, 2810 North Commerce Parkway, Miramar, FL, 33025, USA.
Current address: Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.

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: 43.16 kDa 
• Atom Count: 2,884 
• Modeled Residue Count: 327 
• 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	Bos taurus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PKI peptide	B	18	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q3SX13 (Bos taurus) Explore Q3SX13  Go to UniProtKB:  Q3SX13

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9D1	C [auth A]	3-({[6-(pyridin-4-yl)-1,3-benzothiazol-2-yl][2-(pyrrolidin-1-yl)ethyl]amino}methyl)phenol C25 H26 N4 O S HCJQJVYIAVXTLD-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.276 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.857	α = 90
b = 72.96	β = 90
c = 77.348	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
DENZO	data collection
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-31 
Deposition Author(s): Judge, R.A.

Revision History  

• Version 1.0: 2018-01-31
  Type: Initial release
  
• Version 1.1: 2018-02-14
  Changes: Database references
• Version 1.2: 2018-04-04
  Changes: Data collection, Database references
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Structure summary