agatolimod   Click here for help

GtoPdb Ligand ID: 9843

Synonyms: CpG 7909 | CpG7909 | PF 3512676 | PF-3512676 | ProMune | VaxImmune
Immunopharmacology Ligand
Compound class: Synthetic organic
Comment: Agatolimod is synthetic CpG oligodeoxynucleotide that acts as a TLR9 agonist [3]. We show the parent molecule, whereas the USAN specifies agatolimod sodium (PubChem CID 56841789), and the synonyms we list may also refer to the sodium congener. Its nucleotide sequence is d(P-thio)(T-C-G-T-C-G-T-T-T-T-G-T-C-G-T-T-T-T-G-T-C-G-T-T).
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 165
Hydrogen bond donors 55
Rotatable bonds 143
Topological polar surface area 3684.42
Molecular weight 7701.8
XLogP 18.21
No. Lipinski's rules broken 4
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1O)n1cc(C)c(=O)[nH]c1=O)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cnc2c1nc(N)[nH]c2=O)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1cc(C)c(=O)[nH]c1=O)O)n1cc(C)c(=O)[nH]c1=O)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cnc(c1C)C(=O)NC(=C)N)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O
Isomeric SMILES OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1OP(=S)(OCC1OC(CC1O)n1cc(C)c(=O)[nH]c1=O)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cnc2c1nc(N)[nH]c2=O)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1cc(C)c(=O)[nH]c1=O)O)n1cc(C)c(=O)[nH]c1=O)O)n1cc(C)c(nc1=O)N)O)n1cc(C)c(nc1=O)N)O)n1cnc(c1C)C(=O)NC(=C)N)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)n1cnc2c1nc(N)[nH]c2=O)O)n1ccc(nc1=O)N)O)n1cc(C)c(=O)[nH]c1=O
InChI Key GUVMFDICMFQHSZ-UHFFFAOYSA-N
Selectivity at catalytic receptors
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
TLR9 Hs Agonist Agonist - - - 3
⤷ [3]