6KZD

Crystal structure of TRKc in complex with 3-((6-(4-aminophenyl)imidazo[1,2-a]pyrazin-3-yl)ethynyl)- N-(3-isopropyl-5-((4-methylpiperazin-1-yl)methyl)phenyl)-2- methylbenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report



Literature

Design, synthesis and biological evaluation of 3-(imidazo[1,2-a]pyrazin-3-ylethynyl)-2-methylbenzamides as potent and selective pan-tropomyosin receptor kinase (TRK) inhibitors.

Cui, S.Wang, Y.Wang, Y.Tang, X.Ren, X.Zhang, L.Xu, Y.Zhang, Z.Zhang, Z.M.Lu, X.Ding, K.

(2019) Eur J Med Chem 179: 470-482

  • DOI: 10.1016/j.ejmech.2019.06.064
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A series of 3-(imidazo[1,2-a]pyrazin-3-ylethynyl)-2-methylbenzamides was designed and synthesized as new tropomyosin receptor kinases (Trks) inhibitors by utilizing a structure-guided optimization strategy. One of the most potent compounds 9o suppres ...

    A series of 3-(imidazo[1,2-a]pyrazin-3-ylethynyl)-2-methylbenzamides was designed and synthesized as new tropomyosin receptor kinases (Trks) inhibitors by utilizing a structure-guided optimization strategy. One of the most potent compounds 9o suppressed TrkA/B/C with IC 50 values of 2.65, 10.47 and 2.95 nM, respectively. The compound dose-dependently inhibited brain-derived neurotrophic factor (BDNF)-mediated TrkB activation and suppressed migration and invasion of SH-SY5Y-TrkB neuroblastoma cells expressing high level of TrkB. Inhibitor 9o also inhibited the proliferation of SH-SY5Y-TrkB cells with an IC 50 value of 58 nM, which was comparable to that of an US FDA recently approved drug LOXO-101. Compound 9o may serve as a new lead compound for further anti-cancer drug discovery.


    Organizational Affiliation

    International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, No. 601 Huangpu Avenue West, Guangzhou, 510632, China. Electronic address: dingke@jnu.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NT-3 growth factor receptor
A
312Homo sapiensMutation(s): 0 
Gene Names: NTRK3TRKC
EC: 2.7.10.1
Find proteins for Q16288 (Homo sapiens)
Go to UniProtKB:  Q16288
NIH Common Fund Data Resources
PHAROS  Q16288
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DZ6
Query on DZ6

Download CCD File 
A
3-[2-[6-(4-aminophenyl)imidazo[1,2-a]pyrazin-3-yl]ethynyl]-2-methyl-~{N}-[3-(4-methylpiperazin-1-yl)-5-propan-2-yl-phenyl]benzamide
C36 H37 N7 O
VBGZPGTYAGJBAX-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.695α = 90
b = 54.569β = 90
c = 108.842γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-09-23 
  • Released Date: 2019-10-09 
  • Deposition Author(s): Wang, Y., Zhang, Z.M.

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release