4QBZ

Crystal structure of human TLR8 in complex with DS-802


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

wwPDB Validation 3D Report Full Report



Literature

Determinants of Activity at Human Toll-like Receptors 7 and 8: Quantitative Structure-Activity Relationship (QSAR) of Diverse Heterocyclic Scaffolds

Yoo, E.Salunke, D.B.Sil, D.Guo, X.Salyer, A.C.D.Hermanson, A.R.Kumar, M.Malladi, S.S.Balakrishna, R.Thompson, W.H.Tanji, H.Ohto, U.Shimizu, T.David, S.A.

(2014) J Med Chem 57: 7955-7970

  • DOI: 10.1021/jm500744f
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Toll-like receptor (TLR) 7 and 8 agonists are potential vaccine adjuvants, since they directly activate APCs and enhance Th1-driven immune responses. Previous SAR investigations in several scaffolds of small molecule TLR7/8 activators pointed to the ...

    Toll-like receptor (TLR) 7 and 8 agonists are potential vaccine adjuvants, since they directly activate APCs and enhance Th1-driven immune responses. Previous SAR investigations in several scaffolds of small molecule TLR7/8 activators pointed to the strict dependence of the selectivity for TLR7 vis-à-vis TLR8 on the electronic configurations of the heterocyclic systems, which we sought to examine quantitatively with the goal of developing "heuristics" to define structural requisites governing activity at TLR7 and/or TLR8. We undertook a scaffold-hopping approach, entailing the syntheses and biological evaluations of 13 different chemotypes. Crystal structures of TLR8 in complex with the two most active compounds confirmed important binding interactions playing a key role in ligand occupancy and biological activity. Density functional theory based quantum chemical calculations on these compounds followed by linear discriminant analyses permitted the classification of inactive, TLR8-active, and TLR7/8 dual-active compounds, confirming the critical role of partial charges in determining biological activity.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Kansas , Multidisciplinary Research Building, Room 320D, 2030 Becker Drive, Lawrence, Kansas 66047, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 8
A, B
811Homo sapiensMutation(s): 0 
Gene Names: TLR8UNQ249/PRO286
Find proteins for Q9NR97 (Homo sapiens)
Go to UniProtKB:  Q9NR97
NIH Common Fund Data Resources
PHAROS  Q9NR97
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D80
Query on D80

Download CCD File 
A, B
2-butyl[1,3]oxazolo[4,5-c]quinolin-4-amine
C14 H15 N3 O
XGNXMXDDPAAWFU-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
BMA
Query on BMA

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

Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.153α = 90
b = 156.716β = 77.1
c = 86.156γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release