Biological Assembly 1  

 3D View: Structure | Validation Report | Ligand Interaction

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: 43.29 kDa 
• Atom Count: 2956 
• Modelled Residue Count: 356 
• Deposited Residue Count: 371 
• Unique protein chains: 2

2OJF

Crystal structure of Protein Kinase A in complex with Pyridine-Pyrazolopyridine based inhibitors

• DOI: 10.2210/pdb2OJF/pdb

• Classification: TRANSFERASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2007-01-12 Released: 2007-03-20 
• Deposition Author(s): Stoll, V.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.265 

Literature

Design and synthesis of pyridine-pyrazolopyridine-based inhibitors of protein kinase B/Akt.

Zhu, G.D., Gong, J., Gandhi, V.B., Woods, K., Luo, Y., Liu, X., Guan, R., Klinghofer, V., Johnson, E.F., Stoll, V.S., Mamo, M., Li, Q., Rosenberg, S.H., Giranda, V.L.

(2007) Bioorg Med Chem 15: 2441-2452

• PubMed: 17258463 
• DOI: 10.1016/j.bmc.2007.01.010
• Primary Citation of Related Structures:  
  2OH0, 2OJF


• PubMed Abstract: 
  

Thr-211 is one of three different amino acid residues in the kinase domain of protein kinase B/Akt as compared to protein kinase A (PKA), a closely related analog in the same AGC family. In an attempt to improve the potency and selectivity of our indazole-pyridine series of Akt inhibitors over PKA, efforts have focused on the incorporation of a chemical functionality to interact with the hydroxy group of Thr-211. Several substituents including an oxygen anion, amino, and nitro groups have been introduced at the C-6 position of the indazole scaffold, leading to a significant drop in Akt potency. Incorporation of a nitrogen atom into the phenyl ring at the same position (i.e., 9f) maintained the Akt activity and, in some cases, improved the selectivity over PKA. The structure-activity relationships of the new pyridine-pyrazolopyridine series of Akt inhibitors and their structural features when bound to PKA are also discussed.

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Organizational Affiliation: 

Cancer Research, GPRD, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6101, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase, alpha-catalytic subunit	A [auth E]	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
Inhibitory peptide	B [auth I]	20	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4PY (Subject of Investigation/LOI)	C [auth E]	(2S)-1-(6H-INDOL-3-YL)-3-{[5-(7H-PYRAZOLO[3,4-C]PYRIDIN-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE C22 H20 N6 O CCIACUJJBPSOHE-KRWDZBQOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4PY	PDBBind:  2OJF	IC50: 110 (nM) from 1 assay(s)
	Binding MOAD:  2OJF	IC50: 110 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.290 
• R-Value Work: 0.265 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.762	α = 90
b = 75.447	β = 90
c = 80.397	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-12 
• Released Date: 2007-03-20 
Deposition Author(s): Stoll, V.S.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance