6E59

Crystal structure of the human NK1 tachykinin receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the human NK1tachykinin receptor.

Yin, J.Chapman, K.Clark, L.D.Shao, Z.Borek, D.Xu, Q.Wang, J.Rosenbaum, D.M.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 13264-13269

  • DOI: 10.1073/pnas.1812717115

  • PubMed Abstract: 
  • The NK <sub>1 </sub> tachykinin G-protein-coupled receptor (GPCR) binds substance P, the first neuropeptide to be discovered in mammals. Through activation of NK <sub>1 </sub>R, substance P modulates a wide variety of physiological and disease proces ...

    The NK 1 tachykinin G-protein-coupled receptor (GPCR) binds substance P, the first neuropeptide to be discovered in mammals. Through activation of NK 1 R, substance P modulates a wide variety of physiological and disease processes including nociception, inflammation, and depression. Human NK 1 R (hNK 1 R) modulators have shown promise in clinical trials for migraine, depression, and emesis. However, the only currently approved drugs targeting hNK 1 R are inhibitors for chemotherapy-induced nausea and vomiting (CINV). To better understand the molecular basis of ligand recognition and selectivity, we solved the crystal structure of hNK 1 R bound to the inhibitor L760735, a close analog of the drug aprepitant. Our crystal structure reveals the basis for antagonist interaction in the deep and narrow orthosteric pocket of the receptor. We used our structure as a template for computational docking and molecular-dynamics simulations to dissect the energetic importance of binding pocket interactions and model the binding of aprepitant. The structure of hNK 1 R is a valuable tool in the further development of tachykinin receptor modulators for multiple clinical applications.


    Organizational Affiliation

    School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261.,GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Substance-P receptor, GlgA glycogen synthase, Substance-P receptor chimera
A
542Pyrococcus abyssi (strain GE5 / Orsay)Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: TACR1 (NK1R, TAC1R)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
NK1 tachykinin (neurokinin) receptor with bound inhibitor L760735
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2J8
Find proteins for P25103 (Homo sapiens)
Go to Gene View: TACR1
Go to UniProtKB:  P25103
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L76
Query on L76

Download SDF File 
Download CCD File 
A
1-(4-{[(2R,3S)-2-{(1R)-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy}-3-(4-fluorophenyl)morpholin-4-yl]methyl}-1H-1,2,3-triazol-5-yl)-N,N-dimethylmethanamine
C26 H28 F7 N5 O2
USRYEHHMJIRICK-ZNZBMKLDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.789α = 90.00
b = 61.975β = 100.18
c = 142.942γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesR01-NS103939
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM079383
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR21-GM097617

Revision History 

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references
  • Version 1.2: 2019-01-09
    Type: Data collection, Database references