6D26

Crystal structure of the prostaglandin D2 receptor CRTH2 with fevipiprant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

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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: https://doi.org/10.1016/j.molcel.2018.08.009
  • Primary Citation of Related Structures:  
    6D26, 6D27

  • PubMed Abstract: 

    • 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 ...

    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. Electronic address: chengzh@pitt.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Prostaglandin D2 receptor 2, Endolysin chimeraA470Homo sapiens, Tequatrovirus T4Mutation(s): 3 
Gene Names: PTGDR2, CRTH2, DL1R, GPR44, E, T4Tp126
EC: 3.2.1.17
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5Y4 (Homo sapiens)
Explore Q9Y5Y4 
Go to UniProtKB:  Q9Y5Y4
PHAROS:  Q9Y5Y4
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720Q9Y5Y4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSY
Query on FSY
Download Ideal Coordinates CCD File 
B [auth A]fevipiprant
C19 H17 F3 N2 O4 S
GFPPXZDRVCSVNR-UHFFFAOYSA-N		 Ligand Interaction
OLA
Query on OLA
Download Ideal Coordinates CCD File 
R [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N		 Ligand Interaction
PGE
Query on PGE
Download Ideal Coordinates CCD File 
Q [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N		 Ligand Interaction
SIN
Query on SIN
Download Ideal Coordinates CCD File 
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A]		SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
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],
I [auth A],
J [auth A],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
PGO
Query on PGO
Download Ideal Coordinates CCD File 
S [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
FSY BindingDB:  6D26 Ki: 4 (nM) from 1 assay(s)
Kd: 1 (nM) from 1 assay(s)
IC50: min: 0.4, max: 3.1 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.457α = 90
b = 61.71β = 90
c = 266.517γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence