5WYX

Crystal structure of human TLR8 in complex with CU-CPT8m


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Small-molecule inhibition of TLR8 through stabilization of its resting state

Zhang, S.Hu, Z.Tanji, H.Jiang, S.Das, N.Li, J.Sakaniwa, K.Jin, J.Bian, Y.Ohto, U.Shimizu, T.Yin, H.

(2018) Nat. Chem. Biol. 14: 58-64

  • DOI: 10.1038/nchembio.2518
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endosomal Toll-like receptors (TLR3, TLR7, TLR8, and TLR9) are highly analogous sensors for various viral or bacterial RNA and DNA molecular patterns. Nonetheless, few small molecules can selectively modulate these TLRs. In this manuscript, we identi ...

    Endosomal Toll-like receptors (TLR3, TLR7, TLR8, and TLR9) are highly analogous sensors for various viral or bacterial RNA and DNA molecular patterns. Nonetheless, few small molecules can selectively modulate these TLRs. In this manuscript, we identified the first human TLR8-specific small-molecule antagonists via a novel inhibition mechanism. Crystal structures of two distinct TLR8-ligand complexes validated a unique binding site on the protein-protein interface of the TLR8 homodimer. Upon binding to this new site, the small-molecule ligands stabilize the preformed TLR8 dimer in its resting state, preventing activation. As a proof of concept of their therapeutic potential, we have demonstrated that these drug-like inhibitors are able to suppress TLR8-mediated proinflammatory signaling in various cell lines, human primary cells, and patient specimens. These results not only suggest a novel strategy for TLR inhibitor design, but also shed critical mechanistic insight into these clinically important immune receptors.


    Organizational Affiliation

    School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, China.,Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.,School of Pharmaceutical Sciences, Center of Basic Molecular Science, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, China.,Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital and Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology and Clinical Immunology (Ministry of Education), Beijing, China.,Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.,Department of Orthopedics, Peking Union Medical College Hospital, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 8
A, B
811Homo sapiensMutation(s): 0 
Gene Names: TLR8
Find proteins for Q9NR97 (Homo sapiens)
Go to Gene View: TLR8
Go to UniProtKB:  Q9NR97
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
CU8
Query on CU8

Download SDF File 
Download CCD File 
A, B
7-(3-methylphenyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide
C14 H12 N4 O
HNKGGVGQAVODNJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.201 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 144.144α = 90.00
b = 99.149β = 108.07
c = 140.247γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references