The structure of TrkA kinase bound to the inhibitor 4-naphthalen-1-yl-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.168 

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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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor291Homo sapiensMutation(s): 0 
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
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
31X BindingDB:  4PMS Kd: 7.9 (nM) from 1 assay(s)
IC50: 2300 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.168 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.78α = 90
b = 75.78β = 90
c = 112.19γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

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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: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2015-02-25
    Changes: Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy