SEQ-9   Click here for help

GtoPdb Ligand ID: 13159

Synonyms: sequanamycin 9
PDB Ligand
Compound class: Synthetic organic
Comment: SEQ-9 is the orally bioavailable, advanced lead from the sequanamycins, a class of macrolide antibacterial compounds with potent activity against Mycobacterium tuberculosis [2]. It is one of the structures claimed in Sanofi's patent WO2014044645 [1].
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 Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/). 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 22
Hydrogen bond donors 4
Rotatable bonds 23
Topological polar surface area 301.68
Molecular weight 1243.55
XLogP 4.33
No. Lipinski's rules broken 3

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
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.

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)

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Canonical SMILES CC(C)CC(=O)O[C@@H]1[C@@H](C)[C@@H]([C@@H](C)CO[C@H]2[C@@H]([C@@H]([C@@H]([C@@H](C)O2)O)OC)OC)OC(=O)[C@H](C)[C@H]([C@H](C)[C@H]([C@@H](C)C[C@@](C)(C(=O)[C@@H]1C)OC(=O)NC(C)(C)CNS(=O)(=O)C3=CC=CC=C3)O[C@H]4[C@@H](/C(=N/OC)/C[C@@H](C)O4)O)O[C@H]5C[C@@H](C)N(C)C[C@H](C)O5
Isomeric SMILES C[C@@H]1C[C@@H](O[C@H](CN1C)C)O[C@H]2[C@@H]([C@H]([C@H](C[C@](C(=O)[C@@H]([C@@H]([C@H]([C@H](OC(=O)[C@@H]2C)[C@@H](C)CO[C@H]3[C@@H]([C@@H]([C@@H]([C@H](O3)C)O)OC)OC)C)OC(=O)CC(C)C)C)(C)OC(=O)NC(C)(C)CNS(=O)(=O)C4=CC=CC=C4)C)O[C@H]5[C@@H](/C(=N/OC)/C[C@H](O5)C)O)C
InChI InChI=1S/C61H102N4O20S/c1-32(2)25-45(66)81-51-39(9)50(34(4)30-77-58-54(75-18)53(74-17)47(67)42(12)80-58)83-56(70)41(11)52(82-46-26-35(5)65(16)29-37(7)78-46)38(8)49(84-57-48(68)44(64-76-19)27-36(6)79-57)33(3)28-61(15,55(69)40(51)10)85-59(71)63-60(13,14)31-62-86(72,73)43-23-21-20-22-24-43/h20-24,32-42,46-54,57-58,62,67-68H,25-31H2,1-19H3,(H,63,71)/b64-44+/t33-,34-,35+,36+,37-,38+,39-,40+,41+,42+,46-,47+,48+,49-,50+,51+,52-,53+,54+,57-,58+,61-/m0/s1
InChI Key IXJRUHKGLMWLLP-XMRFQGNKSA-N

Generated using the Chemistry Development Kit (CDK) (Willighagen EL et al. Journal of Cheminformatics vol. 9:33. 2017, doi:10.1186/s13321-017-0220-4; https://cdk.github.io/)
Bioactivity Comments
Inhibition of translation by SEQ-9 is similar against the native and methylated Mycobacterium tuberculosis ribosome with an IC50 of 0.075 μM and 0.064 μM respectively [2].
The compound has potent in vitro activity against replicating (MIC of 0.7 μM) and non-replicating (MIC of 0.6 μM) M. tuberculosis H37Rv, M. tuberculosis H37Rv growth within murine macrophage-like cells (MIC of 0.15 μM) and against drug-susceptible and drug-resistant clinical isolates (MIC of 0.5-1.4 μM) [2]. SEQ-9 also demonstrates in vivo efficacy, as a single agent and in combination, when tested in mouse models of tuberculosis infection [2].