4PMS

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


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: 10.1021/jm5006429
  • Primary Citation of Related Structures:  

  • 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 coll ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
High affinity nerve growth factor receptor
A
291Homo 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
31X
Query on 31X

Download SDF File 
Download CCD File 
A
4-(naphthalen-1-yl)-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid
C27 H18 N4 O3
BUVASZPZZZNEAY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
31XIC50: 2300 nM (100) BINDINGDB
31XKd: 7.9 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.164 
  • Space Group: P 64
Unit Cell:
Length (Å)Angle (°)
a = 75.780α = 90.00
b = 75.780β = 90.00
c = 112.190γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XSCALEdata reduction
BUSTERrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-05-22 
  • Released Date: 2014-06-18 
  • Deposition Author(s): Su, H.P.

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references
  • Version 1.2: 2015-02-04
    Type: Derived calculations
  • Version 1.3: 2015-02-25
    Type: Derived calculations