9MHY | pdb_00009mhy

Human TLR8 ectodomain with small molecule agonist 1

PDB DOI: https://doi.org/10.2210/pdb9MHY/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2024-12-12 Released: 2025-03-05
Deposition Author(s): Critton, D.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.223 (Depositor), 0.229 (DCC)
R-Value Work:
0.201 (Depositor), 0.204 (DCC)
R-Value Observed:
0.202 (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

PubMed: 39811121 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.4c00463
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 194.02 kDa
Atom Count: 13,784
Modeled Residue Count: 1,494
Deposited Residue Count: 1,614
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 8	A, B	807	Homo sapiens	Mutation(s): 0 Gene Names: TLR8, UNQ249/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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NR97
Glycosylation
Glycosylation Sites: 12	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q9NR97-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	C, F	5	N/A	N-Glycosylation	Interactions Focus chain C Focus chain F Interactions & Density Focus chain C Focus chain F

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, G, H	3	N/A	N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain G Focus chain H Interactions & Density Focus chain D Focus chain E Focus chain G Focus chain H

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BLN (Subject of Investigation/LOI) Query on A1BLN Download:Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain T [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain T [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain T [auth A]	EA [auth B], T [auth A]	(3S,4R)-4-[({3-[(5-amino-7-{[(3S)-1-hydroxyhexan-3-yl]amino}-1H-pyrazolo[4,3-d]pyrimidin-1-yl)methyl]-4-methoxyphenyl}methyl)amino]oxolan-3-ol C₂₄ H₃₅ N₇ O₄ INQBZKHDECICSJ-DFQSSKMNSA-N		Interactions Focus chain EA [auth B] Focus chain T [auth A] Interactions & Density Focus chain EA [auth B] Focus chain T [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	AA [auth B] BA [auth B] CA [auth B] I [auth A] J [auth A] AA [auth B], BA [auth B], CA [auth B], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	DA [auth B], R [auth A], S [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain DA [auth B] Focus chain R [auth A] Focus chain S [auth A]