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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.bmcl.2016.04.021

  • 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 dihydrobenzothi ...

    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 Neuroscience Research, Merck Research Laboratories, West Point, PA 19486, United States.,Department of Chemistry Modeling and Informatics, Merck Research Laboratories, West Point, PA 19486, United States. Electronic address: john_sanders@merck.com.,Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, United States. Electronic address: thomas_greshock@merck.com.,Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, United States.,Department of In Vitro Pharmacology, Merck Research Laboratories, West Point, PA 19486, United States.,Department of Drug Metabolism, Merck Research Laboratories, West Point, PA 19486, United States.,Department of Structural Chemistry, Merck Research Laboratories, West Point, PA 19486, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity nerve growth factor receptor
A
296Homo sapiensMutation(s): 0 
Gene Names: NTRK1 (MTC, TRK, TRKA)
EC: 2.7.10.1
Find proteins for P04629 (Homo sapiens)
Go to Gene View: NTRK1
Go to UniProtKB:  P04629
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
69C
Query on 69C

Download SDF File 
Download CCD File 
A
(6R)-3-(methylsulfanyl)-6-phenyl-1-(1H-pyrazol-3-yl)-6,7-dihydrothieno[3,4-c]pyridin-4(5H)-one
C17 H15 N3 O S2
JFNXRABTLWJEOU-CYBMUJFWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.178 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 75.884α = 90.00
b = 75.884β = 90.00
c = 112.712γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-18 
  • Released Date: 2017-08-09 
  • Deposition Author(s): Su, H.P.

Revision History 

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