Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 43.70 kDa 
• Atom Count: 3436 
• Modelled Residue Count: 357 
• Deposited Residue Count: 371 
• Unique protein chains: 2

3ZO4

The Synthesis and Evaluation of Diazaspirocyclic Protein Kinase Inhibitors

• PDB DOI: 10.2210/pdb3ZO4/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Bos taurus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

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:  
  3ZO1, 3ZO2, 3ZO3, 3ZO4


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT ALPHA	A	351	Bos taurus	Mutation(s): 0  Gene Names: PRKACA EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA	B [auth I]	20	Bos taurus	Mutation(s): 0  Gene Names: PKIA
UniProt
Find proteins for Q3SX13 (Bos taurus) Explore Q3SX13  Go to UniProtKB:  Q3SX13

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QWI	D [auth A]	6-(4-PHENYL-1,9-DIAZASPIRO[5.5]UNDECAN-9-YL)-9H-PURINE C20 H24 N6 BBLBYIXSHRFYPM-MRXNPFEDSA-N
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-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

Binding Affinity Annotations
ID	Source	Binding Affinity
QWI	PDBBind:  3ZO4	IC50: 149 (nM) from 1 assay(s)
	Binding MOAD:  3ZO4	IC50: 149 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.195 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.44	α = 90
b = 75.73	β = 90
c = 80.37	γ = 90

Software Package:

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

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
  Changes: Database references
• Version 1.2: 2013-08-28
  Changes: Database references
• Version 1.3: 2018-03-28
  Changes: Data collection, Database references
• Version 1.4: 2019-04-03
  Changes: Data collection, Derived calculations, Experimental preparation