The Crystal Structure of Human Neuropeptide Y Y1 Receptor with BMS-193885

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 

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Structural basis of ligand binding modes at the neuropeptide Y Y1receptor

Yang, Z.Han, S.Keller, M.Kaiser, A.Bender, B.J.Bosse, M.Burkert, K.Kogler, L.M.Wifling, D.Bernhardt, G.Plank, N.Littmann, T.Schmidt, P.Yi, C.Li, B.Ye, S.Zhang, R.Xu, B.Larhammar, D.Stevens, R.C.Huster, D.Meiler, J.Zhao, Q.Beck-Sickinger, A.G.Buschauer, A.Wu, B.

(2018) Nature 556: 520-524

  • DOI: https://doi.org/10.1038/s41586-018-0046-x
  • Primary Citation of Related Structures:  
    5ZBH, 5ZBQ

  • PubMed Abstract: 

    Neuropeptide Y (NPY) receptors belong to the G-protein-coupled receptor superfamily and have important roles in food intake, anxiety and cancer biology 1,2 . The NPY-Y receptor system has emerged as one of the most complex networks with three peptide ligands (NPY, peptide YY and pancreatic polypeptide) binding to four receptors in most mammals, namely the Y 1 , Y 2 , Y 4 and Y 5 receptors, with different affinity and selectivity 3 . NPY is the most powerful stimulant of food intake and this effect is primarily mediated by the Y 1 receptor (Y 1 R) 4 . A number of peptides and small-molecule compounds have been characterized as Y 1 R antagonists and have shown clinical potential in the treatment of obesity 4 , tumour 1 and bone loss 5 . However, their clinical usage has been hampered by low potency and selectivity, poor brain penetration ability or lack of oral bioavailability 6 . Here we report crystal structures of the human Y 1 R bound to the two selective antagonists UR-MK299 and BMS-193885 at 2.7 and 3.0 Å resolution, respectively. The structures combined with mutagenesis studies reveal the binding modes of Y 1 R to several structurally diverse antagonists and the determinants of ligand selectivity. The Y 1 R structure and molecular docking of the endogenous agonist NPY, together with nuclear magnetic resonance, photo-crosslinking and functional studies, provide insights into the binding behaviour of the agonist and for the first time, to our knowledge, determine the interaction of its N terminus with the receptor. These insights into Y 1 R can enable structure-based drug discovery that targets NPY receptors.

  • Organizational Affiliation

    Chinese Academy of Sciences Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Neuropeptide Y receptor type 1,T4 Lysozyme,Neuropeptide Y receptor type 1527Homo sapiensEnterobacteria phage T4TMutation(s): 3 
Gene Names: NPY1RNPYRNPYY1eT4Tp126
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P25929 (Homo sapiens)
Explore P25929 
Go to UniProtKB:  P25929
GTEx:  ENSG00000164128 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720P25929
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 9AF

Download Ideal Coordinates CCD File 
B [auth A]dimethyl 4-{3-[({3-[4-(3-methoxyphenyl)piperidin-1-yl]propyl}carbamoyl)amino]phenyl}-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate
C33 H42 N4 O6
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.58α = 90
b = 126.24β = 90
c = 169.82γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Database references