6HD4

ABL1 IN COMPLEX WITH COMPOUND 7 AND IMATINIB (STI-571)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Asciminib (ABL001), an Allosteric Inhibitor of the Tyrosine Kinase Activity of BCR-ABL1.

Schoepfer, J.Jahnke, W.Berellini, G.Buonamici, S.Cotesta, S.Cowan-Jacob, S.W.Dodd, S.Drueckes, P.Fabbro, D.Gabriel, T.Groell, J.M.Grotzfeld, R.M.Hassan, A.Q.Henry, C.Iyer, V.Jones, D.Lombardo, F.Loo, A.Manley, P.W.Pelle, X.Rummel, G.Salem, B.Warmuth, M.Wylie, A.A.Zoller, T.Marzinzik, A.L.Furet, P.

(2018) J. Med. Chem. 61: 8120-8135

  • DOI: 10.1021/acs.jmedchem.8b01040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chronic myelogenous leukemia (CML) arises from the constitutive activity of the BCR-ABL1 oncoprotein. Tyrosine kinase inhibitors (TKIs) that target the ATP-binding site have transformed CML into a chronic manageable disease. However, some patients de ...

    Chronic myelogenous leukemia (CML) arises from the constitutive activity of the BCR-ABL1 oncoprotein. Tyrosine kinase inhibitors (TKIs) that target the ATP-binding site have transformed CML into a chronic manageable disease. However, some patients develop drug resistance due to ATP-site mutations impeding drug binding. We describe the discovery of asciminib (ABL001), the first allosteric BCR-ABL1 inhibitor to reach the clinic. Asciminib binds to the myristate pocket of BCR-ABL1 and maintains activity against TKI-resistant ATP-site mutations. Although resistance can emerge due to myristate-site mutations, these are sensitive to ATP-competitive inhibitors so that combinations of asciminib with ATP-competitive TKIs suppress the emergence of resistance. Fragment-based screening using NMR and X-ray yielded ligands for the myristate pocket. An NMR-based conformational assay guided the transformation of these inactive ligands into ABL1 inhibitors. Further structure-based optimization for potency, physicochemical, pharmacokinetic, and drug-like properties, culminated in asciminib, which is currently undergoing clinical studies in CML patients.


    Organizational Affiliation

    Novartis Institutes for BioMedical Research , 250 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States.,Novartis Institutes for BioMedical Research, Novartis Campus , CH-4056 Basel , Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ABL1
A, B
293Mus musculusMutation(s): 0 
Gene Names: Abl1 (Abl)
EC: 2.7.10.2
Find proteins for P00520 (Mus musculus)
Go to UniProtKB:  P00520
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FYW
Query on FYW

Download SDF File 
Download CCD File 
A, B
6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-pyrimidin-5-yl-~{N}-[4-(trifluoromethyloxy)phenyl]pyridine-3-carboxamide
C21 H18 F3 N5 O3
LARFZNXVNANWFD-MRXNPFEDSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
STI
Query on STI

Download SDF File 
Download CCD File 
A, B
4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE
STI-571;IMATINIB
C29 H31 N7 O
KTUFNOKKBVMGRW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.181 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.160α = 73.00
b = 65.025β = 80.52
c = 66.086γ = 84.88
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
BUSTERrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-08-17 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Cowan-Jacob, S.W.

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release