6NPE

C-abl Kinase domain with the activator(cmpd6), 2-cyano-N-(4-(3,4-dichlorophenyl)thiazol-2-yl)acetamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Identification and Optimization of Novel Small c-Abl Kinase Activators Using Fragment and HTS Methodologies.

Simpson, G.L.Bertrand, S.M.Borthwick, J.A.Campobasso, N.Chabanet, J.Chen, S.Coggins, J.Cottom, J.Christensen, S.B.Dawson, H.C.Evans, H.L.Hobbs, A.N.Hong, X.Mangatt, B.Munoz-Muriedas, J.Oliff, A.Qin, D.Scott-Stevens, P.Ward, P.Washio, Y.Yang, J.Young, R.J.

(2019) J Med Chem 62: 2154-2171

  • DOI: 10.1021/acs.jmedchem.8b01872
  • Primary Citation of Related Structures:  
    6NPU, 6NPV, 6NPE

  • PubMed Abstract: 
  • Abelson kinase (c-Abl) is a ubiquitously expressed, nonreceptor tyrosine kinase which plays a key role in cell differentiation and survival. It was hypothesized that transient activation of c-Abl kinase via displacement of the N-terminal autoinhibito ...

    Abelson kinase (c-Abl) is a ubiquitously expressed, nonreceptor tyrosine kinase which plays a key role in cell differentiation and survival. It was hypothesized that transient activation of c-Abl kinase via displacement of the N-terminal autoinhibitory "myristoyl latch", may lead to an increased hematopoietic stem cell differentiation. This would increase the numbers of circulating neutrophils and so be an effective treatment for chemotherapy-induced neutropenia. This paper describes the discovery and optimization of a thiazole series of novel small molecule c-Abl activators, initially identified by a high throughput screening. Subsequently, a scaffold-hop, which exploited the improved physicochemical properties of a dihydropyrazole analogue, identified through fragment screening, delivered potent, soluble, cell-active c-Abl activators, which demonstrated the intracellular activation of c-Abl in vivo.


    Related Citations: 
    • 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

    Organizational Affiliation

    Medicines Research Centre , GlaxoSmithKline R&D , Gunnels Wood Road , Stevenage , Hertfordshire SG1 2NY , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1A, B298Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Explore P00519 
Go to UniProtKB:  P00519
NIH Common Fund Data Resources
PHAROS  P00519
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STI
Query on STI

Download CCD File 
A, 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
 Ligand Interaction
2PE
Query on 2PE

Download CCD File 
B
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
KWD
Query on KWD

Download CCD File 
A, B
2-cyano-~{N}-[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]ethanamide
C12 H7 Cl2 N3 O S
UVZNRMKUEHJMJX-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KWDIC50:  10   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.713α = 90
b = 95.018β = 90
c = 115.697γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-01-17 
  • Released Date: 2019-03-13 
  • Deposition Author(s): campobasso, N.

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection