5I8A

TrkA with (6~{R})-3-methylsulfanyl-6-phenyl-1-(1~{H}-pyrazol-3-yl)-6,7-dihydro-5~{H}-thieno[3,4-c]pyridin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Potent, selective and orally bioavailable leucine-rich repeat kinase 2 (LRRK2) inhibitors.

Greshock, T.J.Sanders, J.M.Drolet, R.E.Rajapakse, H.A.Chang, R.K.Kim, B.Rada, V.L.Tiscia, H.E.Su, H.Lai, M.T.Sur, S.M.Sanchez, R.I.Bilodeau, M.T.Renger, J.J.Kern, J.T.McCauley, J.A.

(2016) Bioorg Med Chem Lett 26: 2631-2635

  • DOI: https://doi.org/10.1016/j.bmcl.2016.04.021
  • Primary Citation of Related Structures:  
    5I8A

  • PubMed Abstract: 

    Familial Parkinson's disease cases have recently been associated with the leucine rich repeat kinase 2 (LRRK2) gene. It has been hypothesized that inhibition of the LRRK2 protein may have the potential to alter disease pathogenesis. A dihydrobenzothiophene series of potent, selective, orally bioavailable LRRK2 inhibitors were identified from a high-throughput screen of the internal Merck sample collection. Initial SAR studies around the core established the series as a tractable small molecule lead series of LRRK2 inhibitors for potential treatment of Parkinson's disease. It was also found that incorporation of a lactam into the core drastically improved the CNS and DMPK properties of these small molecules.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, United States. Electronic address: thomas_greshock@merck.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor296Homo 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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.884α = 90
b = 75.884β = 90
c = 112.712γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-08-09 
  • Deposition Author(s): Su, H.P.

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references