3PYY

Discovery and Characterization of a Cell-Permeable, Small-molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site

• PDB DOI:  https://doi.org/10.2210/pdb3PYY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2010-12-13 Released: 2011-03-09 
• Deposition Author(s): Yang, J., Campobasso, N., Biju, M.P., Fisher, K., Pan, X.Q., Cottom, J., Galbraith, S., Ho, T., Zhang, H., Hong, X., Ward, P., Hofmann, G., Siegfried, B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Literature

Discovery and Characterization of a Cell-Permeable, Small-Molecule c-Abl Kinase Activator that Binds to the Myristoyl Binding Site.

Yang, J., Campobasso, N., Biju, M.P., Fisher, K., Pan, X.Q., Cottom, J., Galbraith, S., Ho, T., Zhang, H., Hong, X., Ward, P., Hofmann, G., Siegfried, B., Zappacosta, F., Washio, Y., Cao, P., Qu, J., Bertrand, S., Wang, D.Y., Head, M.S., Li, H., Moores, S., Lai, Z., Johanson, K., Burton, G., Erickson-Miller, C., Simpson, G., Tummino, P., Copeland, R.A., Oliff, A.

(2011) Chem Biol 18: 177-186

• PubMed: 21338916 
• DOI: https://doi.org/10.1016/j.chembiol.2010.12.013
• Primary Citation of Related Structures:  
  3PYY


• PubMed Abstract: 
  

c-Abl kinase activity is regulated by a unique mechanism involving the formation of an autoinhibited conformation in which the N-terminal myristoyl group binds intramolecularly to the myristoyl binding site on the kinase domain and induces the bending of the αI helix that creates a docking surface for the SH2 domain. Here, we report a small-molecule c-Abl activator, DPH, that displays potent enzymatic and cellular activity in stimulating c-Abl activation. Structural analyses indicate that DPH binds to the myristoyl binding site and prevents the formation of the bent conformation of the αI helix through steric hindrance, a mode of action distinct from the previously identified allosteric c-Abl inhibitor, GNF-2, that also binds to the myristoyl binding site. DPH represents the first cell-permeable, small-molecule tool compound for c-Abl activation.

---

Organizational Affiliation: 

Oncology Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.87 kDa 
• Atom Count: 4,625 
• Modelled Residue Count: 522 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-abl Abelson murine leukemia viral oncogene homolog 1 isoform b variant	A, B	298	Homo sapiens	Mutation(s): 0  Gene Names: ABL1, ABL, JTK7 EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P00519 (Homo sapiens) Explore P00519  Go to UniProtKB:  P00519
PHAROS:  P00519

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STI	E [auth A], H [auth B]	4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE C29 H31 N7 O KTUFNOKKBVMGRW-UHFFFAOYSA-N
2PE	I [auth B]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N
3YY	F [auth A], K [auth B]	(5R)-5-[3-(4-fluorophenyl)-1-phenyl-1H-pyrazol-4-yl]imidazolidine-2,4-dione C18 H13 F N4 O2 MPQWYPLPWGUMJE-MRXNPFEDSA-N
SO4	C [auth A], D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STI	BindingDB:  3PYY	Ki: min: 13, max: 7000 (nM) from 5 assay(s)
		Kd: min: 1, max: 1.00e+4 (nM) from 36 assay(s)
		IC50: min: 1.1, max: 1.00e+4 (nM) from 60 assay(s)
		EC50: min: 34, max: 1000 (nM) from 4 assay(s)
3YY	PDBBind:  3PYY	Kd: 137 (nM) from 1 assay(s)
	BindingDB:  3PYY	IC50: min: 251, max: 398 (nM) from 2 assay(s)
		EC50: 794 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.204 
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.391	α = 90
b = 95.432	β = 90
c = 115.502	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-09 
Deposition Author(s): Yang, J., Campobasso, N., Biju, M.P., Fisher, K., Pan, X.Q., Cottom, J., Galbraith, S., Ho, T., Zhang, H., Hong, X., Ward, P., Hofmann, G., Siegfried, B.

Revision History  

• Version 1.0: 2011-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary