5KMI

TrkA JM-kinase with 1-(9{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1073/pnas.1611577114
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,Global Chemistry, Merck Research Laboratories (MRL), Merck & Co. Inc., West Point, PA 19486.,In Vitro Pharmacology, MRL, Merck & Co. Inc., West Point, PA 19486.,Screening & Protein Sciences, MRL, Merck & Co. Inc., West Point, PA 19486.,Neuroscience Discovery, MRL, Merck & Co. Inc., West Point, PA 19486.,In Vitro Pharmacology, MRL, Merck & Co. Inc., Boston, MA 02115.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity nerve growth factor receptor
A
329Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6UE
Query on 6UE

Download SDF File 
Download CCD File 
A
1-(9~{H}-fluoren-9-yl)-3-(2-methyl-4-phenyl-pyrimidin-5-yl)urea
C25 H20 N4 O
PKOROKYRNIDSPX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.208 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 52.065α = 90.00
b = 52.065β = 90.00
c = 227.191γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
BUSTER-TNTrefinement
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-06-27 
  • Released Date: 2016-12-28 
  • Deposition Author(s): Su, H.P.

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-18
    Type: Database references
  • Version 1.2: 2017-02-01
    Type: Database references