5AAA

Structure of L1198F Mutant Human Anaplastic Lymphoma Kinase in Complex with Crizotinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Resensitization to Crizotinib by the Lorlatinib Alk Resistance Mutation L1198F.

Shaw, A.T.Friboulet, L.Leshchiner, I.Gainor, J.F.Bergqvist, S.Brooun, A.Burke, B.J.Deng, Y.Liu, W.Dardaei, L.Frias, R.L.Schultz, K.R.Logan, J.James, L.P.Smeal, T.Timofeevski, S.Katayama, R.Iafrate, A.J.Le, L.Mctigue, M.Getz, G.Johnson, T.W.Engelman, J.A.

(2016) N Engl J Med 374: 54

  • DOI: 10.1056/NEJMoa1508887
  • Primary Citation of Related Structures:  
    5A9U, 5AAB, 5AAA, 5AAC, 5AA8, 5AA9

  • PubMed Abstract: 
  • In a patient who had metastatic anaplastic lymphoma kinase (ALK)-rearranged lung cancer, resistance to crizotinib developed because of a mutation in the ALK kinase domain. This mutation is predicted to result in a substitution of cysteine by tyrosine ...

    In a patient who had metastatic anaplastic lymphoma kinase (ALK)-rearranged lung cancer, resistance to crizotinib developed because of a mutation in the ALK kinase domain. This mutation is predicted to result in a substitution of cysteine by tyrosine at amino acid residue 1156 (C1156Y). Her tumor did not respond to a second-generation ALK inhibitor, but it did respond to lorlatinib (PF-06463922), a third-generation inhibitor. When her tumor relapsed, sequencing of the resistant tumor revealed an ALK L1198F mutation in addition to the C1156Y mutation. The L1198F substitution confers resistance to lorlatinib through steric interference with drug binding. However, L1198F paradoxically enhances binding to crizotinib, negating the effect of C1156Y and resensitizing resistant cancers to crizotinib. The patient received crizotinib again, and her cancer-related symptoms and liver failure resolved. (Funded by Pfizer and others; ClinicalTrials.gov number, NCT01970865.).


    Organizational Affiliation

    Massachusetts General Hospital Cancer Center (A.T.S., L.F., J.F.G., L.D., R.L.F., K.R.S., J.L., G.G., J.A.E.) and the Department of Pathology (A.J.I., L.L., G.G.), Massachusetts General Hospital, Boston, and the Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge (I.L., G.G.) - all in Massachusetts; Pfizer Worldwide Research and Development, La Jolla, CA (S.B., A.B., B.J.B., Y.-L.D., W.L., L.P.J., T.S., S.T., M.M., T.W.J.); and the Japanese Foundation for Cancer Research, Tokyo (R.K.).



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALK TYROSINE KINASE RECEPTORA327Homo sapiensMutation(s): 1 
Gene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
NIH Common Fund Data Resources
PHAROS  Q9UM73
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGH
Query on VGH

Download CCD File 
A
3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
C21 H22 Cl2 F N5 O
KTEIFNKAUNYNJU-GFCCVEGCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VGHIC50:  51   nM  BindingDB
VGHKi:  0.3799999952316284   nM  Binding MOAD
VGHIC50:  28   nM  BindingDB
VGHIC50:  32   nM  BindingDB
VGHEC50:  22840   nM  BindingDB
VGHIC50:  36   nM  BindingDB
VGHIC50:  80   nM  BindingDB
VGHIC50:  2.0999999046325684   nM  BindingDB
VGHIC50:  110   nM  BindingDB
VGHIC50:  1   nM  BindingDB
VGHIC50:  72   nM  BindingDB
VGHIC50:  78   nM  BindingDB
VGHIC50:  17.299999237060547   nM  BindingDB
VGHIC50:  165   nM  BindingDB
VGHIC50:  188   nM  BindingDB
VGHIC50:  200   nM  BindingDB
VGHIC50:  220   nM  BindingDB
VGHIC50:  133   nM  BindingDB
VGHIC50:  148   nM  BindingDB
VGHIC50:  151   nM  BindingDB
VGHIC50:  337   nM  BindingDB
VGHIC50:  353   nM  BindingDB
VGHIC50:  355   nM  BindingDB
VGHKd:  3.299999952316284   nM  BindingDB
VGHIC50:  626   nM  BindingDB
VGHIC50:  0.6399999856948853   nM  BindingDB
VGHIC50:  7.400000095367432   nM  BindingDB
VGHIC50:  843   nM  BindingDB
VGHEC50:  2042   nM  BindingDB
VGHIC50:  478   nM  BindingDB
VGHIC50:  2   nM  BindingDB
VGHIC50:  600   nM  BindingDB
VGHIC50:  605   nM  BindingDB
VGHIC50:  5   nM  BindingDB
VGHKd:  3.5999999046325684   nM  BindingDB
VGHIC50:  1600   nM  BindingDB
VGHIC50:  1.2000000476837158   nM  BindingDB
VGHIC50:  17.600000381469727   nM  BindingDB
VGHIC50:  972   nM  BindingDB
VGHIC50:  1026   nM  BindingDB
VGHIC50:  1148   nM  BindingDB
VGHEC50:  575   nM  BindingDB
VGHIC50:  11   nM  BindingDB
VGHIC50:  3039   nM  BindingDB
VGHKd:  4.400000095367432   nM  BindingDB
VGHIC50:  2.700000047683716   nM  BindingDB
VGHIC50:  2.9000000953674316   nM  BindingDB
VGHIC50:  20   nM  BindingDB
VGHKi:  8.199999809265137   nM  BindingDB
VGHIC50:  24   nM  BindingDB
VGHIC50:  25   nM  BindingDB
VGHKi:  0.7400000095367432   nM  BindingDB
VGHIC50:  14   nM  BindingDB
VGHIC50:  7.670000076293945   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.471α = 90
b = 57.281β = 90
c = 104.702γ = 90
Software Package:
Software NamePurpose
CNXrefinement
AutoPROCdata reduction
Aimlessdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2017-06-14
    Changes: Data collection, Other
  • Version 1.2: 2018-07-04
    Changes: Data collection
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation