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 

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Ligand Structure Quality Assessment 


This is version 1.3 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)  |  3D 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
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens)
Explore P31749 
Go to UniProtKB:  P31749
PHAROS:  P31749
GTEx:  ENSG00000142208 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31749
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GSK3-beta peptideB10N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • 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		A L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
WFE BindingDB:  3MVH IC50: min: 0.5, max: 310 (nM) from 4 assay(s)
Binding MOAD:  3MVH IC50: 0.5 (nM) from 1 assay(s)
PDBBind:  3MVH IC50: 0.5 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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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
  • Version 1.3: 2021-10-06
    Changes: Database references, Derived calculations