6NPE | pdb_00006npe

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 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6NPE

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.8b01872
  • Primary Citation Related Structures: 
    6NPE, 6NPU, 6NPV

  • 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 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.


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

Macromolecule Content 

  • Total Structure Weight: 71.83 kDa 
  • Atom Count: 4,564 
  • Modeled Residue Count: 520 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1
A, B
298Homo sapiensMutation(s): 0 
Gene Names: ABL1ABLJTK7
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
GTEx:  ENSG00000097007 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
STI

Query on STI



Download:Ideal Coordinates CCD File
E [auth A],
I [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

Query on 2PE



Download:Ideal Coordinates CCD File
K [auth B]NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
KWD
(Subject of Investigation/LOI)

Query on KWD



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
2-cyano-~{N}-[4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]ethanamide
C12 H7 Cl2 N3 O S
UVZNRMKUEHJMJX-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.212 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
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



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Data collection
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Structure summary