3QKM

Spirocyclic sulfonamides as AKT inhibitors

• PDB DOI:  https://doi.org/10.2210/pdb3QKM/pdb

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


• Deposited: 2011-02-01 Released: 2011-04-06 
• Deposition Author(s): Xu, R., Banka, A., Blake, J.F., Mitchell, I.S., Wallace, E.M., Gloor, S.L., Martinson, M., Risom, T., Gross, S.D., Morales, T., Vigers, G.P.A., Brandhuber, B.J., Skelton, N.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Discovery of spirocyclic sulfonamides as potent Akt inhibitors with exquisite selectivity against PKA.

Xu, R., Banka, A., Blake, J.F., Mitchell, I.S., Wallace, E.M., Bencsik, J.R., Kallan, N.C., Spencer, K.L., Gloor, S.L., Martinson, M., Risom, T., Gross, S.D., Morales, T.H., Wu, W.I., Vigers, G.P., Brandhuber, B.J., Skelton, N.J.

(2011) Bioorg Med Chem Lett 21: 2335-2340

• PubMed: 21420856 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.098
• Primary Citation of Related Structures:  
  3QKM


• PubMed Abstract: 
  

  We describe the design and synthesis of novel bicyclic spiro sulfonamides as potent Akt inhibitors. Through structure-based rational design, we have successfully improved PKA selectivity of previously disclosed spirochromanes. Representative compounds showed favorable Akt potency while exhibiting up to 1000-fold selectivity against PKA.

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Organizational Affiliation: 

Array BioPharma Inc., 3200 Walnut Street, Boulder, CO 80301, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 40.05 kDa 
• Atom Count: 3,045 
• Modelled Residue Count: 330 
• Deposited Residue Count: 341 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAC-alpha serine/threonine-protein kinase	A	341	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SM9	B [auth A]	N-(2-ethoxyethyl)-N-{(2S)-2-hydroxy-3-[(5R)-2-(quinazolin-4-yl)-2,7-diazaspiro[4.5]dec-7-yl]propyl}-2,6-dimethylbenzenesulfonamide C31 H43 N5 O4 S ABPGHPHYGKUEIO-SUYBVONHSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
SM9	Binding MOAD:  3QKM	IC50: 38 (nM) from 1 assay(s)
	PDBBind:  3QKM	IC50: 38 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.252 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.043	α = 90
b = 57.938	β = 90
c = 149.981	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Xu, R., Banka, A., Blake, J.F., Mitchell, I.S., Wallace, E.M., Gloor, S.L., Martinson, M., Risom, T., Gross, S.D., Morales, T., Vigers, G.P.A., Brandhuber, B.J., Skelton, N.J.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance