9W0L | pdb_00009w0l

S1P3 in complex with CYM52581 and spm242

• PDB DOI: https://doi.org/10.2210/pdb9W0L/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens, Niallia circulans
• Expression System: Puma concolor
• Mutation(s): No 


• Deposited: 2025-07-24 Released: 2026-06-03 
• Deposition Author(s): Beili, W., Qiang, Z., Qiuxiang, T.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.281 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Structural basis of allosteric and bitopic ligands binding in sphingosine-1-phosphate receptors 2 and 3.

Wu, Y., Chen, Q., Wang, H., Liu, K., Wei, J., Wang, M., Chen, K., Zhu, Y., Han, S., Yi, C., Ma, L., Schnapp, G., Pautsch, A., Gnamm, C., Grauert, M., Schmidt, E., Tan, Q., Wu, B., Zhao, Q.

(2025) Protein Cell 

• PubMed: 40851516 
• DOI: https://doi.org/10.1093/procel/pwaf068
• Primary Citation Related Structures: 
  9W0H, 9W0L, 9W0M, 9W0O

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Organizational Affiliation: 
• State Key Laboratory of Drug Research and State Key Laboratory of Chemistry Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
University of Chinese Academy of Sciences, Beijing 100864, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
Lingang Laboratory, Shanghai 200031, China.
Boehringer-Ingelheim Pharma GmbH & Co. KG, Department of Medicinal Chemistry, Biberach 88397, Germany.
Boehringer-Ingelheim Pharma GmbH & Co. KG, Department of Drug Discovery Sciences, Biberach 88397, Germany.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China.
Zhongshan Institute of Drug Discovery, SIMM, CAS, Zhongshan 528400, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 55.27 kDa 
• Atom Count: 3,748 
• Modeled Residue Count: 477 
• Deposited Residue Count: 484 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sphingosine 1-phosphate receptor 3,Endo-1,4-beta-xylanase	A	484	Homo sapiens, Niallia circulans	Mutation(s): 0  Gene Names: S1PR3, C9orf108, C9orf47, EDG3, xlnA EC: 3.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q99500 (Homo sapiens) Explore Q99500  Go to UniProtKB:  Q99500
PHAROS:  Q99500 GTEx:  ENSG00000213694
Find proteins for P09850 (Niallia circulans) Explore P09850  Go to UniProtKB:  P09850
UniProt Groups	Q99500P09850

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EUD( Subject of Investigation/LOI)	C [auth A]	~{N}-[(~{R})-(5-bromanylpyridin-2-yl)-(3,4-dichlorophenyl)methyl]-4-cyano-3-fluoranyl-benzamide C20 H11 Br Cl2 F N3 O XTEYPDFMLGCQTR-LJQANCHMSA-N
A1EUC( Subject of Investigation/LOI)	B [auth A]	[(2~{R})-2-azanyl-4-[2-chloranyl-4-(3-hydroxyphenyl)sulfanyl-phenyl]-2-(hydroxymethyl)butyl] dihydrogen phosphate C17 H21 Cl N O6 P S YKFYJMGZQBDOPG-QGZVFWFLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.281 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.57	α = 90
b = 299.58	β = 90
c = 67.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-06-03 
Deposition Author(s): Beili, W., Qiang, Z., Qiuxiang, T.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2026-06-03
  Type: Initial release