3QKK

Spirochromane Akt Inhibitors

• PDB DOI: https://doi.org/10.2210/pdb3QKK/pdb

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


• Deposited: 2011-02-01 Released: 2011-03-30 
• Deposition Author(s): Kallan, N.C., Spencer, K.L., Blake, J.F., Xu, R., Heizer, J., Bencsik, J.R., Mitchell, I.S., 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: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Discovery and SAR of spirochromane Akt inhibitors.

Kallan, N.C., Spencer, K.L., Blake, J.F., Xu, R., Heizer, J., Bencsik, J.R., Mitchell, I.S., 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: 2410-2414

• PubMed: 21392984 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.073
• Primary Citation of Related Structures:  
  3QKK, 3QKL


• PubMed Abstract: 
  

  A novel series of spirochromane pan-Akt inhibitors is reported. SAR optimization furnished compounds with improved enzyme potencies and excellent selectivity over the related AGC kinase PKA. Attempted replacement of the phenol hinge binder provided compounds with excellent Akt enzyme and cell activities but greatly diminished selectivity over 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: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 41.14 kDa 
• Atom Count: 2,914 
• Modelled Residue Count: 337 
• Deposited Residue Count: 351 
• Unique protein chains: 2

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 GTEx:  ENSG00000142208

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GSK-3 beta peptide	B [auth C]	10	Homo sapiens	Mutation(s): 0  Gene Names: GSK3B
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841  Go to UniProtKB:  P49841
PHAROS:  P49841 GTEx:  ENSG00000082701

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SMH	C [auth A]	N-(2-ethoxyethyl)-N-{(2S)-2-hydroxy-3-[(2R)-6-hydroxy-4-oxo-3,4-dihydro-1'H-spiro[chromene-2,3'-piperidin]-1'-yl]propyl}-2,6-dimethylbenzenesulfonamide C28 H38 N2 O7 S ONZIIEDMJXLRAD-NEKDWFFYSA-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
SMH	PDBBind:  3QKK	IC50: 300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.59	α = 90
b = 56.814	β = 90
c = 151.349	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: 2011-03-30 
Deposition Author(s): Kallan, N.C., Spencer, K.L., Blake, J.F., Xu, R., Heizer, J., Bencsik, J.R., Mitchell, I.S., 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: 2011-03-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance