6BQH

Crystal structure of 5-HT2C in complex with ritanserin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

5-HT2C Receptor Structures Reveal the Structural Basis of GPCR Polypharmacology.

Peng, Y.McCorvy, J.D.Harpsoe, K.Lansu, K.Yuan, S.Popov, P.Qu, L.Pu, M.Che, T.Nikolajsen, L.F.Huang, X.P.Wu, Y.Shen, L.Bjorn-Yoshimoto, W.E.Ding, K.Wacker, D.Han, G.W.Cheng, J.Katritch, V.Jensen, A.A.Hanson, M.A.Zhao, S.Gloriam, D.E.Roth, B.L.Stevens, R.C.Liu, Z.J.

(2018) Cell 172: 719-730.e14

  • DOI: https://doi.org/10.1016/j.cell.2018.01.001
  • Primary Citation of Related Structures:  
    6BQG, 6BQH

  • PubMed Abstract: 

    Drugs frequently require interactions with multiple targets-via a process known as polypharmacology-to achieve their therapeutic actions. Currently, drugs targeting several serotonin receptors, including the 5-HT 2C receptor, are useful for treating obesity, drug abuse, and schizophrenia. The competing challenges of developing selective 5-HT 2C receptor ligands or creating drugs with a defined polypharmacological profile, especially aimed at G protein-coupled receptors (GPCRs), remain extremely difficult. Here, we solved two structures of the 5-HT 2C receptor in complex with the highly promiscuous agonist ergotamine and the 5-HT 2A-C receptor-selective inverse agonist ritanserin at resolutions of 3.0 Å and 2.7 Å, respectively. We analyzed their respective binding poses to provide mechanistic insights into their receptor recognition and opposing pharmacological actions. This study investigates the structural basis of polypharmacology at canonical GPCRs and illustrates how understanding characteristic patterns of ligand-receptor interaction and activation may ultimately facilitate drug design at multiple GPCRs.


  • Organizational Affiliation

    iHuman Institute, ShanghaiTech University, Shanghai 201210, China; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming 650500, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5-hydroxytryptamine receptor 2C,Soluble cytochrome b562452Homo sapiensEscherichia coliMutation(s): 3 
Gene Names: HTR2CHTR1CcybC
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P28335 (Homo sapiens)
Explore P28335 
Go to UniProtKB:  P28335
PHAROS:  P28335
GTEx:  ENSG00000147246 
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7P28335
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E2J (Subject of Investigation/LOI)
Query on E2J

Download Ideal Coordinates CCD File 
B [auth A]6-(2-{4-[bis(4-fluorophenyl)methylidene]piperidin-1-yl}ethyl)-7-methyl-5H-[1,3]thiazolo[3,2-a]pyrimidin-5-one
C27 H25 F2 N3 O S
JUQLTPCYUFPYKE-UHFFFAOYSA-N
OLC
Query on OLC

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.31α = 90
b = 97.05β = 90
c = 150.23γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary