3MVH

Crystal structure of Akt-1-inhibitor complexes

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


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

Literature

Design of selective, ATP-competitive inhibitors of Akt.

Freeman-Cook, K.D., Autry, C., Borzillo, G., Gordon, D., Barbacci-Tobin, E., Bernardo, V., Briere, D., Clark, T., Corbett, M., Jakubczak, J., Kakar, S., Knauth, E., Lippa, B., Luzzio, M.J., Mansour, M., Martinelli, G., Marx, M., Nelson, K., Pandit, J., Rajamohan, F., Robinson, S., Subramanyam, C., Wei, L., Wythes, M., Morris, J.

(2010) J.Med.Chem. 53: 4615-4622

  • DOI: 10.1021/jm1003842
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • This paper describes the design and synthesis of novel, ATP-competitive Akt inhibitors from an elaborated 3-aminopyrrolidine scaffold. Key findings include the discovery of an initial lead that was modestly selective and medicinal chemistry optimizat ...

    This paper describes the design and synthesis of novel, ATP-competitive Akt inhibitors from an elaborated 3-aminopyrrolidine scaffold. Key findings include the discovery of an initial lead that was modestly selective and medicinal chemistry optimization of that lead to provide more selective analogues. Analysis of the data suggested that highly lipophilic analogues would likely suffer from poor overall properties. Central to the discussion is the concept of optimization of lipophilic efficiency and the ability to balance overall druglike propeties with the careful control of lipophilicity in the lead series. Discovery of the nonracemic amide series and subsequent modification produced an advanced analogue that performed well in advanced preclinical assays, including xenograft tumor growth inhibition studies, and this analogue was nominated for clinical development.

    Organizational Affiliation: 

    Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06340, USA. kevin.freeman-cook@pfizer.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
v-akt murine thymoma viral oncogene homolog 1 (AKT1)
A
342Homo sapiensMutation(s): 1 
Gene Names: AKT1 (PKB, RAC)
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Go to Gene View: AKT1
Go to UniProtKB:  P31749
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GSK3-beta peptide
B
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN
Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
WFE
Query on WFE
Download SDF File 
Download CCD File 
A
N-{[(3S)-3-amino-1-(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-3-yl]methyl}-2,4-difluorobenzamide
C20 H22 F2 N6 O
MOZRQQTUYAYCQT-FQEVSTJZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WFEIC50: 12 nM (85) BINDINGDB
WFEIC50: 0.5 nM BINDINGMOAD
WFEIC50: 0.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.354α = 90.00
b = 55.261β = 102.64
c = 92.314γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2010-05-04 
  • Released Date: 2010-06-02 
  • Deposition Author(s): Pandit, J.

Revision History 

  • Version 1.0: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description