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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-023-00617-0
Primary Citation of Related Structures:
8K2W, 8K2X

Organizational Affiliation

Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen, Guangdong, China.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb6	A [auth N]	169	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 P49682 (Homo sapiens) Explore P49682 Go to UniProtKB: P49682
PHAROS: P49682 GTEx: ENSG00000186810
Find proteins for P41145 (Homo sapiens) Explore P41145 Go to UniProtKB: P41145
PHAROS: P41145 GTEx: ENSG00000082556
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P41145P0ABE7P49682
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PCW Query on PCW Download Ideal Coordinates CCD File SDF format, chain D [auth R] MOL2 format, chain D [auth R] mmCIF format, chain D [auth R]	D [auth R]	1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₄₄ H₈₅ N O₈ P SNKAWJBJQDLSFF-NVKMUCNASA-O		Interactions Focus chain D [auth R] Interactions & Density Focus chain D [auth R]
FI6 (Subject of Investigation/LOI) Query on FI6 Download Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R] mmCIF format, chain F [auth R]	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		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]
LPC Query on LPC Download Ideal Coordinates CCD File SDF format, chain E [auth R] MOL2 format, chain E [auth R] mmCIF format, chain E [auth R]	E [auth R]	[1-MYRISTOYL-GLYCEROL-3-YL]PHOSPHONYLCHOLINE C₂₂ H₄₇ N O₇ P VXUOFDJKYGDUJI-OAQYLSRUSA-O		Interactions Focus chain E [auth R] Interactions & Density Focus chain E [auth R]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain C [auth R] MOL2 format, chain C [auth R] mmCIF format, chain C [auth R]	C [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain C [auth R] Interactions & Density Focus chain C [auth R]

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