6HHJ | pdb_00006hhj

Crystal Structure of AKT1 in Complex with Covalent-Allosteric AKT Inhibitor 24b

• PDB DOI: https://doi.org/10.2210/pdb6HHJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-08-28 Released: 2019-02-20 
• Deposition Author(s): Landel, I., Weisner, J., Mueller, M.P., Scheinpflug, R., Rauh, D.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.235 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 30996949 
• DOI: https://doi.org/10.1039/c8sc05212c
• Primary Citation 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.

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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: [e-mail] ; http://www.ddhdortmund.de ; www.twitter.com/DDHDortmund.
Faculty for Chemistry and Pharmacy , Institut für Physikalische und Theoretische Chemie , Universität Würzburg , Emil-Fischer-Strasse 42 , 97074 Würzburg , Germany.
Max-Planck-Institut für Molekulare Physiologie , Abteilung Chemische Biologie , Otto-Hahn-Strasse 11 , 44227 Dortmund , Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 52.36 kDa 
• Atom Count: 3,544 
• Modeled Residue Count: 410 
• Deposited Residue Count: 446 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAC-alpha serine/threonine-protein kinase	A	446	Homo sapiens	Mutation(s): 3  Gene Names: 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4H	B [auth A]	~{N}-[1-methyl-2-oxidanylidene-3-[1-[[4-(5-oxidanylidene-3-phenyl-6~{H}-1,6-naphthyridin-2-yl)phenyl]methyl]piperidin-4-yl]benzimidazol-5-yl]propanamide C37 H36 N6 O3 NOAOWOIAXARUHL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.235 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.05	α = 90
b = 71.37	β = 90
c = 90.96	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-02-20 
Deposition Author(s): Landel, I., Weisner, J., Mueller, M.P., Scheinpflug, R., Rauh, D.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	BMBF 01GS08104
German Federal Ministry for Education and Research	Germany	01ZX1303C

Revision History  

• 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
• Version 1.3: 2024-11-13
  Changes: Structure summary