9MHW | pdb_00009mhw

Human TLR8 ectodomain with small molecule agonist 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.230 (Depositor), 0.224 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structure-Based Design of Novel TLR7/8 Agonist Payloads Enabling an Immunomodulatory Conjugate Approach.

Poudel, Y.B.Lo, J.C.Norris, D.J.Cox, M.He, L.Johnson, W.L.A M Subbaiah, M.Mondal, S.Thangavel, S.Subramani, L.Reddy, M.Jain, S.Weiss, D.R.Sivaprakasam, P.Critton, D.Mulligan, D.Xie, C.Dhar, P.Li, Y.Sega, E.Yamazoe, S.Gavai, A.V.Mathur, A.Zapf, C.W.Chekler, E.P.

(2025) ACS Med Chem Lett 16: 80-88

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00463
  • Primary Citation of Related Structures:  
    9MHV, 9MHW, 9MHX, 9MHY

  • PubMed Abstract: 

    Dual activation of the TLR7 and TLR8 pathways leads to the production of type I interferon and proinflammatory cytokines, resulting in efficient antigen presentation by dendritic cells to promote T-cell priming and antitumor immunity. We developed a novel series of TLR7/8 dual agonists with varying ratios of TLR7 and TLR8 activity for use as payloads for an antibody-drug conjugate approach. The agonist-induced production of several cytokines in human whole blood confirmed their functional activity. Structure-activity relationship studies guided by structure-based drug design are described.


  • Organizational Affiliation

    Bristol Myers Squibb Research & Development, 700 Bay Road, Redwood City, California 94063, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toll-like receptor 8807Homo 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: 12Go to GlyGen: Q9NR97-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(2-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
6N/AN-Glycosylation
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3N/AN-Glycosylation
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BLT (Subject of Investigation/LOI)
Query on A1BLT

Download Ideal Coordinates CCD File 
O [auth A](3S)-3-[(2-amino-5-{[2-methoxy-5-({[(3S)-oxolan-3-yl]amino}methyl)phenyl]methyl}-5H-pyrimido[5,4-b]indol-4-yl)amino]hexan-1-ol
C29 H38 N6 O3
IIFCCEWBZBDLAS-VXKWHMMOSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
N [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.230 (Depositor), 0.224 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 140.073α = 90
b = 100.53β = 121.86
c = 77.913γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release