3ZO4

The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Synthesis and evaluation of heteroaryl substituted diazaspirocycles as scaffolds to probe the ATP-binding site of protein kinases.

Allen, C.E.Chow, C.L.Caldwell, J.J.Westwood, I.M.van Montfort, R.L.Collins, I.

(2013) Bioorg. Med. Chem. 21: 5707-5724

  • DOI: 10.1016/j.bmc.2013.07.021
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • With the success of protein kinase inhibitors as drugs to target cancer, there is a continued need for new kinase inhibitor scaffolds. We have investigated the synthesis and kinase inhibition of new heteroaryl-substituted diazaspirocyclic compounds t ...

    With the success of protein kinase inhibitors as drugs to target cancer, there is a continued need for new kinase inhibitor scaffolds. We have investigated the synthesis and kinase inhibition of new heteroaryl-substituted diazaspirocyclic compounds that mimic ATP. Versatile syntheses of substituted diazaspirocycles through ring-closing metathesis were demonstrated. Diazaspirocycles directly linked to heteroaromatic hinge binder groups provided ligand efficient inhibitors of multiple kinases, suitable as starting points for further optimization. The binding modes of representative diazaspirocyclic motifs were confirmed by protein crystallography. Selectivity profiles were influenced by the hinge binder group and the interactions of basic nitrogen atoms in the scaffold with acidic side-chains of residues in the ATP pocket. The introduction of more complex substitution to the diazaspirocycles increased potency and varied the selectivity profiles of these initial hits through engagement of the P-loop and changes to the spirocycle conformation, demonstrating the potential of these core scaffolds for future application to kinase inhibitor discovery.


    Organizational Affiliation

    Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, Sutton, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA
A
351Bos taurusMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
Find proteins for P00517 (Bos taurus)
Go to Gene View: PRKACA
Go to UniProtKB:  P00517
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA
I
20Bos taurusMutation(s): 0 
Gene Names: PKIA
Find proteins for Q3SX13 (Bos taurus)
Go to Gene View: PKIA
Go to UniProtKB:  Q3SX13
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
QWI
Query on QWI

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Download CCD File 
A
6-(4-PHENYL-1,9-DIAZASPIRO[5.5]UNDECAN-9-YL)-9H-PURINE
C20 H24 N6
BBLBYIXSHRFYPM-MRXNPFEDSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
QWIIC50: 149 nM BINDINGMOAD
QWIIC50: 149 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.440α = 90.00
b = 75.730β = 90.00
c = 80.370γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2013-08-28
    Type: Database references
  • Version 1.3: 2018-03-28
    Type: Data collection, Database references
  • Version 1.4: 2019-04-03
    Type: Data collection, Derived calculations, Experimental preparation