6WML | pdb_00006wml

Human TLR8 bound to the potent agonist, GS-9688 (Selgantolimod)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.255 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of GS-9688 (Selgantolimod) as a Potent and Selective Oral Toll-Like Receptor 8 Agonist for the Treatment of Chronic Hepatitis B.

Mackman, R.L.Mish, M.Chin, G.Perry, J.K.Appleby, T.Aktoudianakis, V.Metobo, S.Pyun, P.Niu, C.Daffis, S.Yu, H.Zheng, J.Villasenor, A.G.Zablocki, J.Chamberlain, J.Jin, H.Lee, G.Suekawa-Pirrone, K.Santos, R.Delaney 4th, W.E.Fletcher, S.P.

(2020) J Med Chem 63: 10188-10203

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00100
  • Primary Citation Related Structures: 
    6WML

  • PubMed Abstract: 

    Toll-like receptor 8 (TLR8) recognizes pathogen-derived single-stranded RNA fragments to trigger innate and adaptive immune responses. Chronic hepatitis B (CHB) is associated with a dysfunctional immune response, and therefore a selective TLR8 agonist may be an effective treatment option. Structure-based optimization of a dual TLR7/8 agonist led to the identification of the selective TLR8 clinical candidate ( R )-2-((2-amino-7-fluoropyrido[3,2- d ]pyrimidin-4-yl)amino)-2-methylhexan-1-ol (GS-9688, ( R )- 7 ). Potent TLR8 agonism (IL-12p40 EC 50 = 220 nM) and >100-fold TLR7 selectivity (IFN-α EC 50 > 50 μM) was observed in human peripheral blood mononuclear cells (PBMCs). The TLR8-ectodomain:( R )- 7 complex confirmed TLR8 binding and a direct ligand interaction with TLR8 residue Asp545. Oral ( R )- 7 had good absorption and high first pass clearance in preclinical species. A reduction in viral markers was observed in HBV-infected primary human hepatocytes treated with media from PBMCs stimulated with ( R )- 7 , supporting the clinical development of ( R )- 7 for the treatment of CHB.


  • Organizational Affiliation
    • Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, California 94404, United States.

Macromolecule Content 

  • Total Structure Weight: 385.5 kDa 
  • Atom Count: 23,787 
  • Modeled Residue Count: 2,883 
  • Deposited Residue Count: 3,244 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Toll-like receptor 8
A, B, C, D
811Homo sapiensMutation(s): 0 
Gene Names: TLR8UNQ249/PRO286
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR97 (Homo sapiens)
Explore Q9NR97 
Go to UniProtKB:  Q9NR97
PHAROS:  Q9NR97
GTEx:  ENSG00000101916 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR97
Glycosylation
Glycosylation Sites: 7Go to GlyGen: Q9NR97-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G22573RC
GlyCosmos: G22573RC
GlyGen: G22573RC
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N/A
Glycosylation Resources
GlyTouCan: G90333CG
GlyCosmos: G90333CG
GlyGen: G90333CG
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, L
G, H, I, J, L, M, O
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K, P
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
N
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
U57
(Subject of Investigation/LOI)

Query on U57



Download:Ideal Coordinates CCD File
GA [auth B],
NA [auth C],
TA [auth D],
X [auth A]
(2R)-2-[(2-amino-7-fluoropyrido[3,2-d]pyrimidin-4-yl)amino]-2-methylhexan-1-ol
C14 H20 F N5 O
HTCJUBZBSJQWBW-CQSZACIVSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
DA [auth B]
EA [auth B]
FA [auth B]
IA [auth C]
AA [auth B],
DA [auth B],
EA [auth B],
FA [auth B],
IA [auth C],
LA [auth C],
MA [auth C],
OA [auth D],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
U [auth A],
V [auth A],
W [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN

Query on MAN



Download:Ideal Coordinates CCD File
BA [auth B]
CA [auth B]
HA [auth C]
JA [auth C]
KA [auth C]
BA [auth B],
CA [auth B],
HA [auth C],
JA [auth C],
KA [auth C],
PA [auth D],
Q [auth A],
T [auth A],
Y [auth B],
Z [auth B]
alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
U57 BindingDB:  6WML EC50: 220 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.255 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.816α = 90
b = 141.575β = 90.413
c = 171.263γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-03
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary