4CMO

Structure of the Human Anaplastic Lymphoma Kinase in Complex with the inhibitor 2-((1R)-1-((3-amino-6-(2-methoxypyridin-3-yl)pyrazin-2-yl) oxy)ethyl)-4-fluoro-N-methylbenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of (10R)-7-Amino-12-Fluoro-2,10,16-Trimethyl-15-Oxo-10,15,16,17-Tetrahydro-2H-8,4-(Metheno)Pyrazolo[4,3-H][2,5,11]Benzoxadiazacyclotetradecine-3-Carbonitrile (Pf-06463922), a Macrocyclic Inhibitor of Alk/Ros1 with Pre-Clinical Brain Exposure and Broad Spectrum Potency Against Alk-Resistant Mutations.

Johnson, T.W.Richardson, P.F.Bailey, S.Brooun, A.Burke, B.J.Collins, M.R.Cui, J.J.Deal, J.G.Deng, Y.L.Dinh, D.M.Engstrom, L.D.He, M.Hoffman, J.E.Hoffman, R.L.Huang, Q.Kath, J.Kania, R.S.Lam, H.Lam, J.L.Le, P.T.Lingardo, L.Liu, W.Mctigue, M.A.Palmer, C.L.Sach, N.W.Smeal, T.Smith, G.L.Stewart, A.E.Timofeevski, S.L.Zhu, H.Zhu, J.Zou, H.Y.Edwards, M.P.

(2014) J Med Chem 57: 4720

  • DOI: 10.1021/jm500261q
  • Primary Citation of Related Structures:  
    4CLI, 4CLJ, 4CMO, 4CMT, 4CMU, 4CNH, 4CTB, 4CTC, 5KZ0

  • PubMed Abstract: 
  • Although crizotinib demonstrates robust efficacy in anaplastic lymphoma kinase (ALK)-positive non-small-cell lung carcinoma patients, progression during treatment eventually develops. Resistant patient samples revealed a variety of point mutations in the kinase domain of ALK, including the L1196M gatekeeper mutation ...

    Although crizotinib demonstrates robust efficacy in anaplastic lymphoma kinase (ALK)-positive non-small-cell lung carcinoma patients, progression during treatment eventually develops. Resistant patient samples revealed a variety of point mutations in the kinase domain of ALK, including the L1196M gatekeeper mutation. In addition, some patients progress due to cancer metastasis in the brain. Using structure-based drug design, lipophilic efficiency, and physical-property-based optimization, highly potent macrocyclic ALK inhibitors were prepared with good absorption, distribution, metabolism, and excretion (ADME), low propensity for p-glycoprotein 1-mediated efflux, and good passive permeability. These structurally unusual macrocyclic inhibitors were potent against wild-type ALK and clinically reported ALK kinase domain mutations. Significant synthetic challenges were overcome, utilizing novel transformations to enable the use of these macrocycles in drug discovery paradigms. This work led to the discovery of 8k (PF-06463922), combining broad-spectrum potency, central nervous system ADME, and a high degree of kinase selectivity.


    Organizational Affiliation

    La Jolla Laboratories, Pfizer Worldwide Research and Development , 10770 Science Center Drive, San Diego, California 92121, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALK TYROSINE KINASE RECEPTORA327Homo sapiensMutation(s): 0 
Gene Names: ALK
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UM73 (Homo sapiens)
Explore Q9UM73 
Go to UniProtKB:  Q9UM73
PHAROS:  Q9UM73
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YPW (Subject of Investigation/LOI)
Query on YPW

Download Ideal Coordinates CCD File 
B [auth A]2-[(1R)-1-{[3-amino-6-(2-methoxypyridin-3-yl)pyrazin-2-yl]oxy}ethyl]-4-fluoro-N-methylbenzamide
C20 H20 F N5 O3
AMLQLZSHSQNJKQ-LLVKDONJSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
YPW BindingDB:  4CMO Ki: min: 0.85, max: 8.2 (nM) from 2 assay(s)
IC50: min: 16, max: 312 (nM) from 2 assay(s)
Binding MOAD:  4CMO Ki: 0.85 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.509α = 90
b = 57.557β = 90
c = 105.288γ = 90
Software Package:
Software NamePurpose
CNXrefinement
AutoPROCdata reduction
SCALAdata scaling
CNXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-25
    Changes: Database references, Refinement description
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other