Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 30b

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

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Structural and chemical insights into the covalent-allosteric inhibition of the protein kinase Akt.

Uhlenbrock, N.Smith, S.Weisner, J.Landel, I.Lindemann, M.Le, T.A.Hardick, J.Gontla, R.Scheinpflug, R.Czodrowski, P.Janning, P.Depta, L.Quambusch, L.Muller, M.P.Engels, B.Rauh, D.

(2019) Chem Sci 10: 3573-3585

  • DOI: https://doi.org/10.1039/c8sc05212c
  • Primary Citation of Related Structures:  
    6HHG, 6HHH, 6HHI, 6HHJ

  • PubMed Abstract: 

    The Ser/Thr kinase Akt (Protein Kinase B/PKB) is a master switch in cellular signal transduction pathways. Its downstream signaling influences cell proliferation, cell growth, and apoptosis, rendering Akt a prominent drug target. The unique activation mechanism of Akt involves a change of the relative orientation of its N-terminal pleckstrin homology (PH) and the kinase domain and makes this kinase suitable for highly specific allosteric modulation. Here we present a unique set of crystal structures of covalent-allosteric interdomain inhibitors in complex with full-length Akt and report the structure-based design, synthesis, biological and pharmacological evaluation of a focused library of these innovative inhibitors.

  • Organizational Affiliation

    Faculty of Chemistry and Chemical Biology , TU Dortmund University , Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW) , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . Email: daniel.rauh@tu-dortmund.de ; http://www.ddhdortmund.de ; www.twitter.com/DDHDortmund.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RAC-alpha serine/threonine-protein kinase446Homo sapiensMutation(s): 3 
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on G4N

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[1-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl)phenyl]methyl]piperidin-4-yl]-3-(propanoylamino)benzamide
C36 H35 N5 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
G4N BindingDB:  6HHI Kd: 79 (nM) from 1 assay(s)
IC50: 18.2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.17α = 90
b = 70.96β = 90
c = 91.11γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermanyBMBF 01GS08104
German Federal Ministry for Education and ResearchGermany01ZX1303C

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-05-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description