TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-(1-naphthyl)urea

Experimental Data Snapshot

  • Resolution: 2.12 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural characterization of nonactive site, TrkA-selective kinase inhibitors.

Su, H.P.Rickert, K.Burlein, C.Narayan, K.Bukhtiyarova, M.Hurzy, D.M.Stump, C.A.Zhang, X.Reid, J.Krasowska-Zoladek, A.Tummala, S.Shipman, J.M.Kornienko, M.Lemaire, P.A.Krosky, D.Heller, A.Achab, A.Chamberlin, C.Saradjian, P.Sauvagnat, B.Yang, X.Ziebell, M.R.Nickbarg, E.Sanders, J.M.Bilodeau, M.T.Carroll, S.S.Lumb, K.J.Soisson, S.M.Henze, D.A.Cooke, A.J.

(2017) Proc Natl Acad Sci U S A 114: E297-E306

  • DOI: https://doi.org/10.1073/pnas.1611577114
  • Primary Citation of Related Structures:  
    5KMI, 5KMJ, 5KMK, 5KML, 5KMM, 5KMN, 5KMO

  • PubMed Abstract: 

    Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of-but adjacent to-the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.

  • Organizational Affiliation

    Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486; hua-poo_su@merck.com.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
High affinity nerve growth factor receptor329Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens)
Explore P04629 
Go to UniProtKB:  P04629
GTEx:  ENSG00000198400 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04629
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 6UJ

Download Ideal Coordinates CCD File 
B [auth A]1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-naphthalen-1-yl-urea
C22 H18 N4 O
Binding Affinity Annotations 
IDSourceBinding Affinity
6UJ BindingDB:  5KMM IC50: 4100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.12 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.06α = 90
b = 52.06β = 90
c = 226.03γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2016-12-28 
  • Deposition Author(s): Su, H.P.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-02-01
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description