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 PQS (software)

Macromolecule Content

• Total Structure Weight: 41.91 kDa 
• Atom Count: 2959 
• Modelled Residue Count: 356 
• Deposited Residue Count: 356 
• Unique protein chains: 2

2UZV

PKA structures of indazole-pyridine series of AKT inhibitors

• DOI: 10.2210/pdb2UZV/pdb

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


• Deposited: 2007-05-01 Released: 2007-06-05 
• Deposition Author(s): 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., Penning, T.D., Li, Q., Rosenberg, S.H., Giranda, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.316 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 

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

• PubMed: 17523610 
• 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. 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.

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Organizational Affiliation: 

Cancer Research, Preclinical Safety, Structural Biology, Integrative Pharmacology, GPRD, Abbott Laboratories, 100 Abbott Park Road, Abbott Park, Illinois 60064-6101, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA,	A [auth 2]	20	Bos taurus	Mutation(s): 0  Gene Names: PKIA
UniProt
Find proteins for Q3SX13 (Bos taurus) Explore Q3SX13  Go to UniProtKB:  Q3SX13

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT	B [auth A]	336	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SS5 (Subject of Investigation/LOI)	C [auth A]	(2S)-1-[3-(CYCLOHEXYLMETHOXY)PHENYL]-3-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE C29 H34 N4 O2 MFYOLTIJRSXVBH-VWLOTQADSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SS5	BindingDB:  2UZV	IC50: 3000 (nM) from 1 assay(s)
	PDBBind:  2UZV	IC50: 1360 (nM) from 1 assay(s)
	Binding MOAD:  2UZV	IC50: 3000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.316 
• R-Value Work: 0.251 
• R-Value Observed: 0.251 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.755	α = 90
b = 74.748	β = 90
c = 80.049	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-05-01 
• Released Date: 2007-06-05 
Deposition Author(s): 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., Penning, T.D., Li, Q., Rosenberg, S.H., Giranda, V.L.

Revision History  

• 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