9GBE | pdb_00009gbe

Structure of Human Anaplastic Lymphoma Kinase (ALK) harboring the G1202R/L1196M Compound Mutation in Complex with NVL-655


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 
    0.224 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

NVL-655 Is a Selective and Brain-Penetrant Inhibitor of Diverse ALK-Mutant Oncoproteins, Including Lorlatinib-Resistant Compound Mutations.

Lin, J.J.Horan, J.C.Tangpeerachaikul, A.Swalduz, A.Valdivia, A.Johnson, M.L.Besse, B.Camidge, D.R.Fujino, T.Yoda, S.Nguyen-Phuong, L.Mizuta, H.Bigot, L.Nobre, C.Lee, J.B.Yu, M.R.Mente, S.Sun, Y.Kohl, N.E.Porter, J.R.Shair, M.D.Zhu, V.W.Felip, E.Cho, B.C.Friboulet, L.Hata, A.N.Pelish, H.E.Drilon, A.

(2024) Cancer Discov 14: 2367-2386

  • DOI: https://doi.org/10.1158/2159-8290.CD-24-0231
  • Primary Citation Related Structures: 
    9GBE

  • PubMed Abstract: 

    Three generations of tyrosine kinase inhibitors (TKI) have been approved for anaplastic lymphoma kinase (ALK) fusion-positive non-small cell lung cancer. However, none address the combined need for broad resistance coverage, brain activity, and avoidance of clinically dose-limiting TRK inhibition. NVL-655 is a rationally designed TKI with >50-fold selectivity for ALK over 96% of the kinome tested. In vitro, NVL-655 inhibits diverse ALK fusions, activating alterations, and resistance mutations, showing ≥100-fold improved potency against ALKG1202R single and compound mutations over approved ALK TKIs. In vivo, it induces regression across 12 tumor models, including intracranial and patient-derived xenografts. NVL-655 inhibits ALK over TRK with 22-fold to >874-fold selectivity. These preclinical findings are supported by three case studies from an ongoing first-in-human phase I/II trial of NVL-655 which demonstrate preliminary proof-of-concept clinical activity in heavily pretreated patients with ALK fusion-positive non-small cell lung cancer, including in patients with brain metastases and single or compound ALK resistance mutations. Significance: By combining broad activity against single and compound ALK resistance mutations, brain penetrance, and selectivity, NVL-655 addresses key limitations of currently approved ALK inhibitors and has the potential to represent a distinct advancement as a fourth-generation inhibitor for patients with ALK-driven cancers.


  • Organizational Affiliation
    • Massachusetts General Hospital Cancer Center, Boston, Massachusetts.

Macromolecule Content 

  • Total Structure Weight: 39.39 kDa 
  • Atom Count: 2,782 
  • Modeled Residue Count: 304 
  • Deposited Residue Count: 344 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ALK tyrosine kinase receptor344Homo sapiensMutation(s): 2 
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
GTEx:  ENSG00000171094 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UM73
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IJ8
(Subject of Investigation/LOI)

Query on A1IJ8



Download:Ideal Coordinates CCD File
B [auth A]NVL-655
C23 H22 Cl F N6 O
FWZSCAQEBTVTOM-GFCCVEGCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free:  0.224 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.525α = 90
b = 57.198β = 90
c = 105.229γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Database references
  • Version 1.2: 2024-12-11
    Changes: Database references, Structure summary