6D27 | pdb_00006d27

Crystal structure of the prostaglandin D2 receptor CRTH2 with CAY10471

• PDB DOI: https://doi.org/10.2210/pdb6D27/pdb

• Classification: MEMBRANE PROTEIN/ANTAGONIST
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2018-04-13 Released: 2018-10-03 
• Deposition Author(s): Wang, L., Yao, D., Deepak, K., Liu, H., Gong, W., Fan, H., Wei, Z., Zhang, C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free: 
  0.280 (Depositor), 0.282 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.244 (Depositor) 

Starting Model: experimental

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

• PubMed: 30220562 
• DOI: https://doi.org/10.1016/j.molcel.2018.08.009
• Primary Citation 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. 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.

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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; University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
Bioinformatics Institute (BII), Agency for Science, Technology and Research (A(∗)STAR), Singapore 138671, Singapore.
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.
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.
Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China. Electronic address: [e-mail].
Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 54.79 kDa 
• Atom Count: 3,618 
• Modeled Residue Count: 443 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin D2 receptor 2, Endolysin chimera	A	470	Homo sapiens, Tequatrovirus T4	Mutation(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 P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for Q9Y5Y4 (Homo sapiens) Explore Q9Y5Y4  Go to UniProtKB:  Q9Y5Y4
PHAROS:  Q9Y5Y4 GTEx:  ENSG00000183134
UniProt Groups	P00720Q9Y5Y4

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FT4	I [auth A]	[(3R)-3-{[(4-fluorophenyl)sulfonyl](methyl)amino}-1,2,3,4-tetrahydro-9H-carbazol-9-yl]acetic acid C21 H21 F N2 O4 S CANCTKXGRVNXFP-OAHLLOKOSA-N
OLA	K [auth A], L [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
MES	J [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PGE	M [auth A], N [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	S [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PGO	O [auth A], P [auth A], Q [auth A], R [auth A]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
YCM	A	L-PEPTIDE LINKING	C5 H10 N2 O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
FT4	BindingDB:  6D27	Ki: min: 0.6, max: 6 (nM) from 3 assay(s)
		IC50: min: 1.2, max: 3.6 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.74 Å
• R-Value Free:  0.280 (Depositor), 0.282 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.244 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.175	α = 90
b = 62.636	β = 90
c = 272.215	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-10-03 
Deposition Author(s): Wang, L., Yao, D., Deepak, K., Liu, H., Gong, W., Fan, H., Wei, Z., Zhang, C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• 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
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description