6J20

Crystal structure of the human NK1 substance P receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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 NK ...

    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

    University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China. zhaoq@simm.ac.cn.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen, 2200, Denmark.,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China. beiliwu@simm.ac.cn.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. beiliwu@simm.ac.cn.,iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China. wuthrich@scripps.edu.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Pudong, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China. beiliwu@simm.ac.cn.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. zhaoq@simm.ac.cn.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. zhaoq@simm.ac.cn.,School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China. wuthrich@scripps.edu.,iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA. wuthrich@scripps.edu.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China. zhaoq@simm.ac.cn.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. beiliwu@simm.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Substance-P receptor,Endolysin
A
441Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 4 
Gene Names: TACR1 (NK1R, TAC1R), E
EC: 3.2.1.17
Find proteins for P25103 (Homo sapiens)
Go to Gene View: TACR1
Go to UniProtKB:  P25103
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GBQ
Query on GBQ

Download SDF File 
Download 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.233 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.512α = 90.00
b = 102.512β = 90.00
c = 156.962γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



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