6D26

Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.798 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of the Human PGD2Receptor CRTH2 Reveal Novel Mechanisms for Ligand Recognition.

Wang, L.Yao, D.Deepak, R.N.V.K.Liu, H.Xiao, Q.Fan, H.Gong, W.Wei, Z.Zhang, C.

(2018) Mol. Cell 72: 48-59.e4

  • DOI: 10.1016/j.molcel.2018.08.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The signaling of prostaglandin D <sub>2 </sub> (PGD <sub>2 </sub>) through G-protein-coupled receptor (GPCR) CRTH2 is a major pathway in type 2 inflammation. Compelling evidence suggests the therapeutic benefits of blocking CRTH2 signaling in many in ...

    The signaling of prostaglandin D 2 (PGD 2 ) through G-protein-coupled receptor (GPCR) CRTH2 is a major pathway in type 2 inflammation. Compelling evidence suggests the therapeutic benefits of blocking CRTH2 signaling in many inflammatory disorders. Currently, a number of CRTH2 antagonists are under clinical investigation, and one compound, fevipiprant, has advanced to phase 3 clinical trials for asthma. Here, we present the crystal structures of human CRTH2 with two antagonists, fevipiprant and CAY10471. The structures, together with docking and ligand-binding data, reveal a semi-occluded pocket covered by a well-structured amino terminus and different binding modes of chemically diverse CRTH2 antagonists. Structural analysis suggests a ligand entry port and a binding process that is facilitated by opposite charge attraction for PGD 2 , which differs significantly from the binding pose and binding environment of lysophospholipids and endocannabinoids, revealing a new mechanism for lipid recognition by GPCRs.


    Organizational Affiliation

    Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Hefei National Research Center for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.,Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138671, Singapore.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.,Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China. Electronic address: weizy@sustc.edu.cn.,Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address: chengzh@pitt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Prostaglandin D2 receptor 2, Endolysin chimera
A
470Homo sapiensEnterobacteria phage T4
This entity is chimeric
Mutation(s): 2 
Gene Names: PTGDR2 (CRTH2, DL1R, GPR44), E
EC: 3.2.1.17
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
prostaglandin D2 receptor CRTH2 with bound fevipiprant
Find proteins for Q9Y5Y4 (Homo sapiens)
Go to Gene View: PTGDR2
Go to UniProtKB:  Q9Y5Y4
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SIN
Query on SIN

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Download CCD File 
A
SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
 Ligand Interaction
OLA
Query on OLA

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Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
FSY
Query on FSY

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Download CCD File 
A
fevipiprant
(2-methyl-1-{[4-(methylsulfonyl)-2-(trifluoromethyl)phenyl]methyl}-1H-pyrrolo[2,3-b]pyridin-3-yl)acetic acid
C19 H17 F3 N2 O4 S
GFPPXZDRVCSVNR-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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Download CCD File 
A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.798 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.457α = 90.00
b = 61.710β = 90.00
c = 266.517γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina--

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references