4PMT

The structure of TrkA kinase bound to the inhibitor N~4~-(4-morpholin-4-ylphenyl)-N~6~-(pyridin-3-ylmethyl)pyrido[3,2-d]pyrimidine-4,6-diamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain.

Stachel, S.J.Sanders, J.M.Henze, D.A.Rudd, M.T.Su, H.P.Li, Y.Nanda, K.K.Egbertson, M.S.Manley, P.J.Jones, K.L.Brnardic, E.J.Green, A.Grobler, J.A.Hanney, B.Leitl, M.Lai, M.T.Munshi, V.Murphy, D.Rickert, K.Riley, D.Krasowska-Zoladek, A.Daley, C.Zuck, P.Kane, S.A.Bilodeau, M.T.

(2014) J Med Chem 57: 5800-5816

  • DOI: https://doi.org/10.1021/jm5006429
  • Primary Citation of Related Structures:  
    4PMM, 4PMP, 4PMS, 4PMT

  • PubMed Abstract: 

    We have identified several series of small molecule inhibitors of TrkA with unique binding modes. The starting leads were chosen to maximize the structural and binding mode diversity derived from a high throughput screen of our internal compound collection. These leads were optimized for potency and selectivity employing a structure based drug design approach adhering to the principles of ligand efficiency to maximize binding affinity without overly relying on lipophilic interactions. This endeavor resulted in the identification of several small molecule pan-Trk inhibitor series that exhibit high selectivity for TrkA/B/C versus a diverse panel of kinases. We have also demonstrated efficacy in both inflammatory and neuropathic pain models upon oral dosing. Herein we describe the identification process, hit-to-lead progression, and binding profiles of these selective pan-Trk kinase inhibitors.


  • Organizational Affiliation

    Departments of Medicinal Chemistry, Biological Chemistry, Pain & Migraine, Molecular Systems, and Structural Biology, Merck Research Laboratories , P.O. Box 4, West Point, Pennsylvania 19486, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor291Homo sapiensMutation(s): 0 
Gene Names: NTRK1MTCTRKTRKA
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Go to UniProtKB:  P04629
PHAROS:  P04629
GTEx:  ENSG00000198400 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
31Y BindingDB:  4PMT IC50: 997 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.186 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.7α = 90
b = 75.7β = 90
c = 112.68γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-06-18 
  • Deposition Author(s): Su, H.P.

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy