7XAF

The crystal structure of TrkA kinase in complex with 4^6,14-dimethyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-10-oxo-5-oxa-11,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclo- tetradecaphan-2-yne-45-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of the First Highly Selective and Broadly Effective Macrocycle-Based Type II TRK Inhibitors that Overcome Clinically Acquired Resistance.

Wang, Z.Wang, J.Wang, Y.Xiang, S.Song, X.Tu, Z.Zhou, Y.Zhang, Z.M.Zhang, Z.Ding, K.Lu, X.

(2022) J Med Chem 65: 6325-6337

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00308
  • Primary Citation of Related Structures:  
    7XAF

  • PubMed Abstract: 

    Tropomyosin receptor kinase (TRK) secondary mutations mediating acquired resistance, especially at the solvent-front (SF) and the DFG motif, represent an unmet clinical need. Small-molecule macrocyclic kinase inhibitors have displayed significant advantages in overcoming clinical resistance driven by kinase mutations; however, all reported small-molecule macrocyclic TRK inhibitors are all type I inhibitors and are therefore much more sensitive to SF than xDFG mutations. Novel therapeutics for patients with xDFG resistance mutations are urgently needed. We report the first highly selective macrocycle-based potent type II TRK inhibitor, 7b , that exhibits high inhibitory potency toward various TRK fusion protein variants as well as wild type. 7b exhibited potent antiproliferative activity against Ba/F3 cells harboring CD74-TRKA G667C and ETV6-TRKC G696C with half-maximum inhibitory concentration (IC 50 ) values of 6 and 1.7 nM, respectively. More importantly, 7b also showed potent antiproliferative activity against a panel of SF mutants (IC 50 = 5.6-110 nM) and displayed extraordinary kinome selectivity.


  • Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, Guangzhou 510632, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor299Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
PHAROS:  P04629
GTEx:  ENSG00000198400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FKT (Subject of Investigation/LOI)
Query on FKT

Download Ideal Coordinates CCD File 
B [auth A]4^6,14-dimethyl-N-(3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)-10-oxo-5-oxa-11,14-diaza-1(3,6)-imidazo[1,2-b]pyridazina-4(1,3)-benzenacyclo-tetradecaphan-2-yne-45-carboxamide
C35 H33 F3 N8 O3
BGQOUQWQPRPBKN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.1159α = 90
b = 52.1159β = 90
c = 228.483γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrysalisProdata scaling
Cootmodel building
CrysalisProdata reduction
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: 2022-06-01
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description