6E59

Crystal structure of the human NK1 tachykinin receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.3 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
  • Primary Citation of Related Structures:  
    6E59

  • PubMed Abstract: 
  • 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 ...

    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

    Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Substance-P receptor, GlgA glycogen synthase, Substance-P receptor chimeraA542Homo sapiensPyrococcus abyssi GE5Mutation(s): 0 
Gene Names: TACR1NK1RTAC1RPAB2292
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2J8 
Go to UniProtKB:  Q9V2J8
Find proteins for P25103 (Homo sapiens)
Explore P25103 
Go to UniProtKB:  P25103
PHAROS:  P25103
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L76 (Subject of Investigation/LOI)
Query on L76

Download Ideal Coordinates CCD File 
B [auth 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: 3.40 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.251 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.789α = 90
b = 61.975β = 100.18
c = 142.942γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01-NS103939
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM079383
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR21-GM097617

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-12
    Type: Initial release
  • Version 1.1: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-09
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence