8TTY | pdb_00008tty

Crystal structure of monkey TLR7 ectodomain with compound 5

PDB DOI: https://doi.org/10.2210/pdb8TTY/pdb

Classification: IMMUNE SYSTEM
Organism(s): Macaca mulatta
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2023-08-15 Released: 2024-02-07
Deposition Author(s): Critton, D.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.238 (Depositor), 0.236 (DCC)
R-Value Work:
0.205 (Depositor), 0.204 (DCC)
R-Value Observed:
0.206 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of Novel TLR7 Agonists as Systemic Agent for Combination With aPD1 for Use in Immuno-oncology.

Poudel, Y.B., He, L., Cox, M., Zhang, Q., Johnson, W.L., Cong, Q., Cheng, H., Chowdari, N.S., Tarby, C., Donnell, A.F., Broekema, M., O'Malley, D.P., Zhang, Y., A M Subbaiah, M., Kumar, B.V., Subramani, L., Wang, B., Li, Y.X., Sivaprakasam, P., Critton, D., Mulligan, D., Sandhu, B., Xie, C., Ramakrishnan, R., Nagar, J., Dudhgaonkar, S., Oderinde, M.S., Murtaza, A., Schieven, G.L., Mathur, A., Gavai, A.V., Vite, G., Gangwar, S.

(2024) ACS Med Chem Lett 15: 181-188

PubMed: 38352830 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.3c00455
Primary Citation Related Structures:
8TTY, 8TTZ

PubMed Abstract:
We have designed and developed novel and selective TLR7 agonists that exhibited potent receptor activity in a cell-based reporter assay. In vitro , these agonists significantly induced secretion of cytokines IL-6, IL-1β, IL-10, TNFa, IFNa, and IP-10 in human and mouse whole blood. Pharmacokinetic and pharmacodynamic studies in mice showed a significant secretion of IFNα and TNFα cytokines. When combined with aPD1 in a CT-26 tumor model, the lead compound showed strong synergistic antitumor activity with complete tumor regression in 8/10 mice dosed using the intravenous route. Structure-activity relationship studies enabled by structure-based designs of TLR7 agonists are disclosed.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 194.09 kDa
Atom Count: 13,424
Modeled Residue Count: 1,536
Deposited Residue Count: 1,634
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A, B	817	Macaca mulatta	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QEC (Subject of Investigation/LOI) Query on QEC Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain V [auth B] MOL2 format, chain N [auth A] MOL2 format, chain V [auth B] mmCIF format, chain N [auth A] mmCIF format, chain V [auth B]	N [auth A], V [auth B]	N~7~-butyl-2-({4-[(cyclobutylamino)methyl]-2-methoxyphenyl}methyl)-2H-pyrazolo[4,3-d]pyrimidine-5,7-diamine C₂₂ H₃₁ N₇ O CGDCRWDAYYPCJB-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain V [auth B] Interactions & Density Focus chain N [auth A] Focus chain V [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [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], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [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 O [auth B] Focus chain P [auth B] 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] 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 O [auth B] Focus chain P [auth B] 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]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B]	W [auth B], X [auth B], Y [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]