2UZT

PKA structures of AKT, indazole-pyridine inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Syntheses of Potent, Selective, and Orally Bioavailable Indazole-Pyridine Series of Protein Kinase B/Akt Inhibitors with Reduced Hypotension.

Zhu, G.D.Gandhi, V.B.Gong, J.Thomas, S.Woods, K.W.Song, X.Li, T.Diebold, R.B.Luo, Y.Liu, X.Guan, R.Klinghofer, V.Johnson, E.F.Bouska, J.Olson, A.Marsh, K.C.Stoll, V.S.Mamo, M.Polakowski, J.Campbell, T.J.Martin, R.L.Gintant, G.A.Penning, T.D.Li, Q.Rosenberg, S.H.Giranda, V.L.

(2007) J Med Chem 50: 2990

  • DOI: 10.1021/jm0701019
  • Primary Citation of Related Structures:  
    2UZT, 2UZU, 2UZV, 2UZW

  • PubMed Abstract: 
  • Compound 7 was identified as a potent (IC50 = 14 nM), selective, and orally bioavailable (F = 70% in mouse) inhibitor of protein kinase B/Akt. While promising efficacy was observed in vivo, this compound showed effects on depolarization of Purkinje fibers in an in vitro assay and CV hypotension in vivo ...

    Compound 7 was identified as a potent (IC50 = 14 nM), selective, and orally bioavailable (F = 70% in mouse) inhibitor of protein kinase B/Akt. While promising efficacy was observed in vivo, this compound showed effects on depolarization of Purkinje fibers in an in vitro assay and CV hypotension in vivo. Guided by an X-ray structure of 7 bound to protein kinase A, which has 80% homology with Akt in the kinase domain, our efforts have focused on structure-activity relationship (SAR) studies of the phenyl moiety, in an attempt to address the cardiovascular liability and further improve the Akt potency. A novel and efficient synthetic route toward diversely substituted phenyl derivatives of 7 was developed utilizing a copper-mediated aziridine ring-opening reaction as the key step. To improve the selectivity of these Akt inhibitors over other protein kinases, a nitrogen atom was incorporated into selected phenyl analogues of 7 at the C-6 position of the methyl indazole scaffold. These modifications resulted in the discovery of inhibitor 37c with greater potency (IC50 = 0.6 nM vs Akt), selectivity, and improved cardiovascular safety profile. The SARs, pharmacokinetic profile, and CV safety of selected Akt inhibitors will be discussed.


    Organizational Affiliation

    Cancer Research, Preclinical Safety, Structural Biology, Integrative Pharmacology, GPRD, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-6101, USA. gui-dong.zhu@abbott.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNITA336Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus)
Explore P00517 
Go to UniProtKB:  P00517
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00517
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHAB20Bos taurusMutation(s): 0 
Gene Names: PKIA
UniProt
Find proteins for Q3SX13 (Bos taurus)
Explore Q3SX13 
Go to UniProtKB:  Q3SX13
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3SX13
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SS3
Query on SS3

Download Ideal Coordinates CCD File 
C [auth A](2S)-1-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}-3-PHENYLPROPAN-2-AMINE
C22 H22 N4 O
BPNUQXPIQBZCMR-IBGZPJMESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SS3 BindingDB:  2UZT Ki: 16 (nM) from 1 assay(s)
Kd: min: 56, max: 90 (nM) from 2 assay(s)
IC50: 16 (nM) from 1 assay(s)
Binding MOAD:  2UZT IC50: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.273 
  • R-Value Observed: 0.273 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.165α = 90
b = 78.262β = 90
c = 100.846γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance