6J21

Crystal structure of the human NK1 substance P receptor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report



Literature

Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography.

Chen, S., Lu, M., Liu, D., Yang, L., Yi, C., Ma, L., Zhang, H., Liu, Q., Frimurer, T.M., Wang, M.W., Schwartz, T.W., Stevens, R.C., Wu, B., Wuthrich, K., Zhao, Q.

(2019) Nat Commun 10: 638-638

  • DOI: 10.1038/s41467-019-08568-5
  • Primary Citation of Related Structures:  
    6J21, 6J20

  • PubMed Abstract: 

    • Neurokinin 1 receptor (NK1R) has key regulating functions in the central and peripheral nervous systems, and NK1R antagonists such as aprepitant have been approved for treating chemotherapy-induced nausea and vomiting. However, the lack of data on NK1R s ...

    Neurokinin 1 receptor (NK1R) has key regulating functions in the central and peripheral nervous systems, and NK1R antagonists such as aprepitant have been approved for treating chemotherapy-induced nausea and vomiting. However, the lack of data on NK1R structure and biochemistry has limited further drug development targeting this receptor. Here, we combine NMR spectroscopy and X-ray crystallography to provide dynamic and static characterisation of the binding mode of aprepitant in complexes with human NK1R variants. 19 F-NMR showed a slow off-rate in the binding site, where aprepitant occupies multiple substates that exchange with frequencies in the millisecond range. The environment of the bound ligand is affected by the amino acid in position 2.50, which plays a key role in ligand binding and receptor signaling in class A GPCRs. Crystal structures now reveal how receptor signaling relates to the conformation of the conserved NP 7.50 xxY motif in transmembrane helix VII.

    Organizational Affiliation: 

    CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. zhaoq@simm.ac.cn.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Substance-P receptor,Endolysin A441Homo sapiens, Escherichia virus T4Mutation(s): 5 
Gene Names: TACR1, NK1R, TAC1R, E, T4Tp126
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for P25103 (Homo sapiens)
Explore P25103 
Go to UniProtKB:  P25103
NIH Common Fund Data Resources
PHAROS:  P25103
GTEx:  ENSG00000115353
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GBQ
Query on GBQ
Download Ideal Coordinates CCD File 
A
5-[[(2~{R},3~{S})-2-[(1~{R})-1-[3,5-bis(trifluoromethyl)phenyl]ethoxy]-3-(4-fluorophenyl)morpholin-4-yl]methyl]-1,2-dihydro-1,2,4-triazol-3-one
C23 H21 F7 N4 O3
ATALOFNDEOCMKK-OITMNORJSA-N		 Ligand Interaction
OLC
Query on OLC
Download Ideal Coordinates CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.11α = 90
b = 103.11β = 90
c = 158.16γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDB-SSW-SMC054

Revision History 

  • Version 1.0: 2019-03-06
    Type: Initial release