2OJF

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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

  • DOI: 10.1016/j.bmc.2007.01.010
  • Primary Citation of Related Structures:  

  • 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 ind ...

    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.

    Organizational Affiliation: 

    Cancer Research, GPRD, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, IL 60064-6101, USA. gui-dong.zhu@abbott.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunit
E
351Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Go to Gene View: PRKACA
Go to UniProtKB:  P00517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Inhibitory peptide
I
20N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4PY
Query on 4PY
Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4PYIC50: 15 nM BINDINGMOAD
4PYIC50: 110 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.265 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.762α = 90.00
b = 75.447β = 90.00
c = 80.397γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance