8K2W | pdb_00008k2w

Structure of CXCR3 complexed with antagonist AMG487

• PDB DOI: https://doi.org/10.2210/pdb8K2W/pdb
• EM Map EMD-36841: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Lama glama, Escherichia coli, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-07-14 Released: 2023-11-29 
• Deposition Author(s): Jiao, H.Z., Hu, H.L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure basis for the modulation of CXC chemokine receptor 3 by antagonist AMG487.

Jiao, H., Pang, B., Chiang, Y.C., Chen, Q., Pan, Q., Ren, R., Hu, H.

(2023) Cell Discov 9: 119-119

• PubMed: 38012179 
• DOI: https://doi.org/10.1038/s41421-023-00617-0
• Primary Citation Related Structures: 
  8K2W, 8K2X

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Organizational Affiliation: 
• Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China.
School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China.
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China. [e-mail].
Shanghai Qi Zhi Institute, Shanghai, China. [e-mail].
Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China. [e-mail].
School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 77.24 kDa 
• Atom Count: 3,143 
• Modeled Residue Count: 386 
• Deposited Residue Count: 676 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb6	A [auth N]	169	Lama glama	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,C-X-C chemokine receptor type 3,Kappa-type opioid receptor	B [auth R]	507	Escherichia coli, Homo sapiens	Mutation(s): 0  Gene Names: cybC, CXCR3, OPRK1, OPRK Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P41145 (Homo sapiens) Explore P41145  Go to UniProtKB:  P41145
PHAROS:  P41145 GTEx:  ENSG00000082556
Find proteins for P49682 (Homo sapiens) Explore P49682  Go to UniProtKB:  P49682
PHAROS:  P49682 GTEx:  ENSG00000186810
UniProt Groups	P41145P0ABE7P49682

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PCW	D [auth R]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H85 N O8 P SNKAWJBJQDLSFF-NVKMUCNASA-O
FI6 (Subject of Investigation/LOI)	F [auth R]	N-[(1R)-1-[3-(4-ethoxyphenyl)-4-oxidanylidene-pyrido[2,3-d]pyrimidin-2-yl]ethyl]-N-(pyridin-3-ylmethyl)-2-[4-(trifluoromethyloxy)phenyl]ethanamide C32 H28 F3 N5 O4 WQTKNBPCJKRYPA-OAQYLSRUSA-N
LPC	E [auth R]	[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE C22 H47 N O7 P VXUOFDJKYGDUJI-OAQYLSRUSA-O
CLR	C [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FI6	BindingDB:  8K2W	Ki: min: 39.81, max: 158.49 (nM) from 2 assay(s)
		IC50: min: 5, max: 330 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Jiao, H.Z., Hu, H.L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100963
Other private		Ganghong Young Scholar Development Fund

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-23
  Changes: Data collection