Crystal structure of the Neurokinin 1 receptor in complex with the small molecule antagonist CP-99,994

Experimental Data Snapshot

  • Resolution: 3.27 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

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Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists.

Schoppe, J.Ehrenmann, J.Klenk, C.Rucktooa, P.Schutz, M.Dore, A.S.Pluckthun, A.

(2019) Nat Commun 10: 17-17

  • DOI: https://doi.org/10.1038/s41467-018-07939-8
  • Primary Citation of Related Structures:  
    6HLL, 6HLO, 6HLP

  • PubMed Abstract: 

    Neurokinins (or tachykinins) are peptides that modulate a wide variety of human physiology through the neurokinin G protein-coupled receptor family, implicated in a diverse array of pathological processes. Here we report high-resolution crystal structures of the human NK 1 receptor (NK 1 R) bound to two small-molecule antagonist therapeutics - aprepitant and netupitant and the progenitor antagonist CP-99,994. The structures reveal the detailed interactions between clinically approved antagonists and NK 1 R, which induce a distinct receptor conformation resulting in an interhelical hydrogen-bond network that cross-links the extracellular ends of helices V and VI. Furthermore, the high-resolution details of NK 1 R bound to netupitant establish a structural rationale for the lack of basal activity in NK 1 R. Taken together, these co-structures provide a comprehensive structural basis of NK 1 R antagonism and will facilitate the design of new therapeutics targeting the neurokinin receptor family.

  • Organizational Affiliation

    Heptares Therapeutics Zürich AG, Grabenstrasse 11a, 8952, Zürich, Switzerland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Substance-P receptor,GlgA glycogen synthase,Substance-P receptor520Homo sapiensPyrococcus abyssi GE5Mutation(s): 7 
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
GTEx:  ENSG00000115353 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9V2J8P25103
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on GBK

Download Ideal Coordinates CCD File 
B [auth A](2~{S},3~{S})-~{N}-[(2-methoxyphenyl)methyl]-2-phenyl-piperidin-3-amine
C19 H24 N2 O
Binding Affinity Annotations 
IDSourceBinding Affinity
GBK BindingDB:  6HLL Ki: min: 0.17, max: 1.5 (nM) from 8 assay(s)
Kd: 0.32 (nM) from 1 assay(s)
IC50: min: 0.17, max: 2.9 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 3.27 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.996α = 90
b = 122.733β = 90
c = 286.494γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A_153143

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description