Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Macromolecule Content

• Total Structure Weight: 43700.87 
• Atom Count: 2989 
• Residue Count: 371 
• Unique protein chains: 2

3ZO4

The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors

• DOI: 10.2210/pdb3ZO4/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-02-20 Released: 2013-03-06 
• Deposition Author(s): Allen, C.E., Chow, C.L., Caldwell, J.J., Westwood, I.M., van Montfort, R.L., Collins, I.

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Experimental Data Snapshot

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

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

• PubMed: 23920481 
• DOI: 10.1016/j.bmc.2013.07.021
• Primary Citation of Related Structures:  
  3ZO3, 3ZO2, 3ZO1


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA	A	351	Bos taurus	Mutation(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
Molecule	Chains	Sequence Length	Organism	Details
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA	I	20	Bos taurus	Mutation(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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
QWI	A	6-(4-PHENYL-1,9-DIAZASPIRO[5.5]UNDECAN-9-YL)-9H-PURINE C20 H24 N6 BBLBYIXSHRFYPM-MRXNPFEDSA-N
DMS	A	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MPD	A	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
QWI	IC50: 149 nM BINDINGMOAD
QWI	IC50: 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 = 73.440	α = 90.00
b = 75.730	β = 90.00
c = 80.370	γ = 90.00

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
XDS	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-20 
• Released Date: 2013-03-06 
• Deposition Author(s): Allen, C.E., Chow, C.L., Caldwell, J.J., Westwood, I.M., van Montfort, R.L., Collins, I.

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