9MHV | pdb_00009mhv

Monkey TLR7 ectodomain with small molecule agonist 9

PDB DOI: https://doi.org/10.2210/pdb9MHV/pdb

Classification: IMMUNE SYSTEM
Organism(s): Macaca mulatta
Expression System: Drosophila melanogaster
Mutation(s): Yes

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: 2.45 Å
R-Value Free:
0.244 (Depositor), 0.230 (DCC)
R-Value Work:
0.221 (Depositor), 0.208 (DCC)
R-Value Observed:
0.222 (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: 194.48 kDa
Atom Count: 13,134
Modeled Residue Count: 1,536
Deposited Residue Count: 1,634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A, B	817	Macaca mulatta	Mutation(s): 4 Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653 Go to UniProtKB: B3Y653
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3Y653
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
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	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BLT (Subject of Investigation/LOI) Query on A1BLT Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	O [auth A], Y [auth B]	(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		Interactions Focus chain O [auth A] Focus chain Y [auth B] Interactions & Density Focus chain O [auth A] Focus chain Y [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] 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 Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] 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 Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain Z [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth B]	P [auth A], Z [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Z [auth B] Interactions & Density Focus chain P [auth A] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain X [auth B] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B]	N [auth A], X [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain X [auth B] Interactions & Density Focus chain N [auth A] Focus chain X [auth B]