7DDZ

The Crystal Structure of Human Neuropeptide Y Y2 Receptor with JNJ-31020028


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural basis for ligand recognition of the neuropeptide Y Y 2 receptor.

Tang, T.Hartig, C.Chen, Q.Zhao, W.Kaiser, A.Zhang, X.Zhang, H.Qu, H.Yi, C.Ma, L.Han, S.Zhao, Q.Beck-Sickinger, A.G.Wu, B.

(2021) Nat Commun 12: 737-737

  • DOI: 10.1038/s41467-021-21030-9
  • Primary Citation of Related Structures:  
    7DDZ

  • PubMed Abstract: 
  • The human neuropeptide Y (NPY) Y 2 receptor (Y 2 R) plays essential roles in food intake, bone formation and mood regulation, and has been considered an important drug target for obesity and anxiety. However, development of drugs targeting Y 2 R remains challenging with no success in clinical application yet ...

    The human neuropeptide Y (NPY) Y 2 receptor (Y 2 R) plays essential roles in food intake, bone formation and mood regulation, and has been considered an important drug target for obesity and anxiety. However, development of drugs targeting Y 2 R remains challenging with no success in clinical application yet. Here, we report the crystal structure of Y 2 R bound to a selective antagonist JNJ-31020028 at 2.8 Å resolution. The structure reveals molecular details of the ligand-binding mode of Y 2 R. Combined with mutagenesis studies, the Y 2 R structure provides insights into key factors that define antagonistic activity of diverse antagonists. Comparison with the previously determined antagonist-bound Y 1 R structures identified receptor-ligand interactions that play different roles in modulating receptor activation and mediating ligand selectivity. These findings deepen our understanding about molecular mechanisms of ligand recognition and subtype specificity of NPY receptors, and would enable structure-based drug design.


    Organizational Affiliation

    School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China. beiliwu@simm.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Human Neuropeptide Y Y2 Receptor fusion proteinA665Enterobacteria phage RB59Homo sapiensDesulfovibrio vulgaris str. HildenboroughMutation(s): 5 
Gene Names: eRB59_126NPY2RDVU_2680
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P49146 (Homo sapiens)
Explore P49146 
Go to UniProtKB:  P49146
PHAROS:  P49146
Find proteins for P00323 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough))
Explore P00323 
Go to UniProtKB:  P00323
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
H46 (Subject of Investigation/LOI)
Query on H46

Download Ideal Coordinates CCD File 
B [auth A]~{N}-[4-[4-[(1~{S})-2-(diethylamino)-2-oxidanylidene-1-phenyl-ethyl]piperazin-1-yl]-3-fluoranyl-phenyl]-2-pyridin-3-yl-benzamide
C34 H36 F N5 O2
OVUNRYUVDVWTTE-YTTGMZPUSA-N
 Ligand Interaction
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.258 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.42α = 90
b = 50.863β = 90.667
c = 184.629γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31825010
National Science Foundation (NSF, China)China81525024
National Science Foundation (NSF, China)China31700653
Chinese Academy of SciencesChinaXDB37030101

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-27
    Type: Initial release
  • Version 1.1: 2021-02-17
    Changes: Database references