2OH0

Crystal structure of Protein Kinase A in complex with Pyridine-Pyrazolopyridine Based Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.273 

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
2PY
Query on 2PY

Download SDF File 
Download CCD File 
E
(2S)-1-{[5-(1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}-3-[(7AS)-7AH-INDOL-3-YL]PROPAN-2-AMINE
C23 H21 N5 O
CAASENZOSQYNPX-HSTJUUNISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2PYIC50: 18 nM BINDINGMOAD
2PYIC50: 18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.492α = 90.00
b = 74.854β = 90.00
c = 80.165γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-01-09 
  • 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