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 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    5MO4

  • 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 years ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase ABL1A495Homo sapiensMutation(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
GTEx:  ENSG00000097007 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00519
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIL
Query on NIL
Download Ideal Coordinates CCD File 
B [auth A]Nilotinib
C28 H22 F3 N7 O
HHZIURLSWUIHRB-UHFFFAOYSA-N		 Ligand Interaction
AY7
Query on AY7
Download Ideal Coordinates CCD File 
C [auth A]asciminib
C20 H18 Cl F2 N5 O3
VOVZXURTCKPRDQ-CQSZACIVSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NIL BindingDB:  5MO4 Ki: 1 (nM) from 1 assay(s)
Kd: min: 3.6, max: 1.00e+4 (nM) from 15 assay(s)
IC50: min: 0.33, max: 1000 (nM) from 18 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.28α = 90
b = 124.13β = 90
c = 74.66γ = 90
Software Package:
Software NamePurpose
AutoPROCdata reduction
XDSdata reduction
SCALAdata scaling
BUSTERrefinement
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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  (Full details and data files)

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