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 
  • R-Value Observed: 0.181 

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:  
    3MV5, 3MVH, 3MVJ

  • 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 optimization of that lead to provide more selective analogues ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
v-akt murine thymoma viral oncogene homolog 1 (AKT1)A342Homo sapiensMutation(s): 1 
Gene Names: AKT-1, AKT1, PKB, RAC
EC: 2.7.11.1
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
NIH Common Fund Data Resources
PHAROS:  P31749
GTEx:  ENSG00000142208
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GSK3-beta peptideB10N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WFE
Query on WFE
Download Ideal Coordinates CCD File 
 D [auth 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
MN
Query on MN
Download Ideal Coordinates CCD File 
 C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO		AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
WFEIC50 :  0.5   nM  PDBBind
WFEIC50:  9   nM  BindingDB
WFEIC50:  12   nM  BindingDB
WFEIC50:  310   nM  BindingDB
WFEIC50:  0.5   nM  BindingDB
WFEIC50:  0.5   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.354α = 90
b = 55.261β = 102.64
c = 92.314γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


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  (Full details and data files)

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