5MO4

ABL1 kinase (T334I_D382N) in complex with asciminib and nilotinib

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

The allosteric inhibitor ABL001 enables dual targeting of BCR-ABL1.

Wylie, A.A., Schoepfer, J., Jahnke, W., Cowan-Jacob, S.W., Loo, A., Furet, P., Marzinzik, A.L., Pelle, X., Donovan, J., Zhu, W., Buonamici, S., Hassan, A.Q., Lombardo, F., Iyer, V., Palmer, M., Berellini, G., Dodd, S., Thohan, S., Bitter, H., Branford, S., Ross, D.M., Hughes, T.P., Petruzzelli, L., Vanasse, K.G., Warmuth, M., Hofmann, F., Keen, N.J., Sellers, W.R.

(2017) Nature 543: 733-737

  • DOI: 10.1038/nature21702

  • PubMed Abstract: 

    • Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 ...

    Chronic myeloid leukaemia (CML) is driven by the activity of the BCR-ABL1 fusion oncoprotein. ABL1 kinase inhibitors have improved the clinical outcomes for patients with CML, with over 80% of patients treated with imatinib surviving for more than 10 years. Second-generation ABL1 kinase inhibitors induce more potent molecular responses in both previously untreated and imatinib-resistant patients with CML. Studies in patients with chronic-phase CML have shown that around 50% of patients who achieve and maintain undetectable BCR-ABL1 transcript levels for at least 2 years remain disease-free after the withdrawal of treatment. Here we characterize ABL001 (asciminib), a potent and selective allosteric ABL1 inhibitor that is undergoing clinical development testing in patients with CML and Philadelphia chromosome-positive (Ph+) acute lymphoblastic leukaemia. In contrast to catalytic-site ABL1 kinase inhibitors, ABL001 binds to the myristoyl pocket of ABL1 and induces the formation of an inactive kinase conformation. ABL001 and second-generation catalytic inhibitors have similar cellular potencies but distinct patterns of resistance mutations, with genetic barcoding studies revealing pre-existing clonal populations with no shared resistance between ABL001 and the catalytic inhibitor nilotinib. Consistent with this profile, acquired resistance was observed with single-agent therapy in mice; however, the combination of ABL001 and nilotinib led to complete disease control and eradicated CML xenograft tumours without recurrence after the cessation of treatment.

    Organizational Affiliation: 

    Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase ABL1
A
495Homo sapiensMutation(s): 0 
Gene Names: ABL1 (ABL, JTK7)
EC: 2.7.10.2
Find proteins for P00519 (Homo sapiens)
Go to Gene View: ABL1
Go to UniProtKB:  P00519
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIL
Query on NIL
Download SDF File 
Download CCD File 
A
Nilotinib
4-methyl-N-[3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]-3-[(4-pyridin-3-ylpyrimidin-2-yl)amino]benzamide
C28 H22 F3 N7 O
HHZIURLSWUIHRB-UHFFFAOYSA-N
 Ligand Interaction
AY7
Query on AY7
Download SDF File 
Download CCD File 
A
asciminib
C20 H18 Cl F2 N5 O3
VOVZXURTCKPRDQ-CQSZACIVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 118.280α = 90.00
b = 124.130β = 90.00
c = 74.660γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata reduction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2016-12-13 
  • Released Date: 2017-04-05 
  • Deposition Author(s): Cowan-Jacob, S.W.

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references