8Q61 | pdb_00008q61

Co-crystal structure of human AKT2 with compound 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.263 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Identification and development of a subtype-selective allosteric AKT inhibitor suitable for clinical development.

Page, N.Wappett, M.O'Dowd, C.R.O'Rourke, M.Gavory, G.Zhang, L.Rountree, J.S.S.Jordan, L.Barker, O.Gibson, H.Boyd, C.Feutren-Burton, S.McLean, E.Trevitt, G.Harrison, T.

(2022) Sci Rep 12: 15715

  • DOI: https://doi.org/10.1038/s41598-022-20208-5
  • Primary Citation Related Structures: 
    8Q61

  • PubMed Abstract: 

    The serine/threonine protein kinase AKT plays a pivotal role within the PI3K pathway in regulating cellular proliferation and apoptotic cellular functions, and AKT hyper-activation via gene amplification and/or mutation has been implicated in multiple human malignancies. There are 3 AKT isoenzymes (AKT1-3) which mediate critical, non-redundant functions. We present the discovery and development of ALM301, a novel, allosteric, sub-type selective inhibitor of AKT1/2. ALM301 binds in an allosteric pocket created by the combined movement of the PH domain and the catalytic domain, resulting in a DFG out conformation. ALM301 was shown to be highly selective against a panel of over 450 kinases and potently inhibited cellular proliferation. These effects were particularly pronounced in MCF-7 cells containing a PI3KCA mutation. Subsequent cellular downstream pathway analysis in this sensitive cell line revealed potent inhibition of pAKT signalling up to 48 h post dosing. ALM301 treatment was well tolerated in an MCF-7 xenograft model and led to a dose-dependent reduction in tumour growth. Enhanced efficacy was observed in combination with tamoxifen. In summary, ALM301 is a highly specific AKT 1/2 inhibitor with an excellent pharmacological profile suitable for further clinical development.


  • Organizational Affiliation
    • Almac Discovery Ltd, Health Sciences Building, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK.

Macromolecule Content 

  • Total Structure Weight: 56.99 kDa 
  • Atom Count: 3,371 
  • Modeled Residue Count: 384 
  • Deposited Residue Count: 483 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RAC-beta serine/threonine-protein kinase483Homo sapiensMutation(s): 1 
Gene Names: AKT2
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31751 (Homo sapiens)
Explore P31751 
Go to UniProtKB:  P31751
PHAROS:  P31751
GTEx:  ENSG00000105221 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31751
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K06
(Subject of Investigation/LOI)

Query on K06



Download:Ideal Coordinates CCD File
B [auth A]6-[4-(1-azanyl-3-methyl-3-oxidanyl-cyclobutyl)phenyl]-7-phenyl-1-propyl-pyrido[2,3-b][1,4]oxazin-2-one
C27 H29 N3 O3
TVEPNGFDBLRHKR-MCZWQBSQSA-N
MES

Query on MES



Download:Ideal Coordinates CCD File
G [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.263 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.667α = 90
b = 113.885β = 90
c = 73.048γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
MERLOTphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release