8S9H | pdb_00008s9h

Crystal structure of monkey TLR7 ectodomain with compound 14

PDB DOI: https://doi.org/10.2210/pdb8S9H/pdb

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

Deposited: 2023-03-28 Released: 2024-02-07
Deposition Author(s): Critton, D.A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.270 (Depositor), 0.250 (DCC)
R-Value Work:
0.247 (Depositor), 0.230 (DCC)
R-Value Observed:
0.248 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Identification and Optimization of Small Molecule Pyrazolopyrimidine TLR7 Agonists for Applications in Immuno-oncology.

He, L., Zhang, M.Y., Cox, M., Zhang, Q., Donnell, A.F., Zhang, Y., Tarby, C., Gill, P., Subbaiah, M.A.M., Ramar, T., Reddy, M., Puttapaka, V., Li, Y.X., Sivaprakasam, P., Critton, D., Mulligan, D., Xie, C., Ramakrishnan, R., Nagar, J., Dudhgaonkar, S., Murtaza, A., Oderinde, M.S., Schieven, G.L., Mathur, A., Gavai, A.V., Vite, G., Gangwar, S., Poudel, Y.B.

(2024) ACS Med Chem Lett 15: 189-196

PubMed: 38352849 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.3c00456
Primary Citation of Related Structures:
8S9H

PubMed Abstract:
Small molecule toll-like receptor (TLR) 7 agonists have gathered considerable interest as promising therapeutic agents for applications in cancer immunotherapy. Herein, we describe the development and optimization of a series of novel TLR7 agonists through systematic structure-activity relationship studies focusing on modification of the phenylpiperidine side chain. Additional refinement of ADME properties culminated in the discovery of compound 14 , which displayed nanomolar reporter assay activity and favorable drug-like properties. Compound 14 demonstrated excellent in vivo pharmacokinetic/pharmacodynamic profiles and synergistic antitumor activity when administered in combination with aPD1 antibody, suggesting opportunities of employing 14 in immuno-oncology therapies with immune checkpoint blockade agents.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 194.26 kDa
Atom Count: 13,394
Modelled Residue Count: 1,536
Deposited Residue Count: 1,634
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3Y653
Glycosylation
Glycosylation Sites: 9	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence LOADING

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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	3D 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
ZWV (Subject of Investigation/LOI) Query on ZWV Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth B] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] mmCIF format, chain N [auth A] mmCIF format, chain W [auth B]	N [auth A], W [auth B]	(3S)-3-{[5-amino-1-({3-methoxy-5-[1-(oxan-4-yl)piperidin-4-yl]pyridin-2-yl}methyl)-1H-pyrazolo[4,3-d]pyrimidin-7-yl]amino}hexan-1-ol C₂₈ H₄₂ N₈ O₃ RZRJLAWKPZNKQG-NRFANRHFSA-N		Interactions Focus chain N [auth A] Focus chain W [auth B] Interactions & Density Focus chain N [auth A] Focus chain W [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 K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain Q [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 H [auth A] SDF format, chain R [auth B] MOL2 format, chain G [auth A] 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 P [auth B] MOL2 format, chain Q [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 H [auth A] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] 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 P [auth B] mmCIF format, chain Q [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 H [auth A] mmCIF format, chain R [auth B]	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], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [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 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] Focus chain V [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 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] Focus chain V [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain X [auth B] MOL2 format, chain O [auth A] MOL2 format, chain X [auth B] mmCIF format, chain O [auth A] mmCIF format, chain X [auth B]	O [auth A], X [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain O [auth A] Focus chain X [auth B] Interactions & Density Focus chain O [auth A] Focus chain X [auth B]