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tubercidin   Click here for help

GtoPdb Ligand ID: 4755

Synonyms: sparsamycin A
PDB Ligand
Compound class: Natural product
Comment: Tubercidin is an analogue of adenosine. It was originally isolated from the soil-dwelling actinomycete Streptomyces tubercidicus and demonstrates antineoplastic and broad-spectrum antimicrobial activities [1].

tubercidin is commercially available from our sponsors

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 7
Hydrogen bond donors 4
Rotatable bonds 2
Topological polar surface area 126.65
Molecular weight 266.1
XLogP -0.56
No. Lipinski's rules broken 0

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 OCC1OC(C(C1O)O)n1ccc2c1ncnc2N
Isomeric SMILES OC[C@H]1O[C@H]([C@@H]([C@@H]1O)O)n1ccc2c1ncnc2N
InChI InChI=1S/C11H14N4O4/c12-9-5-1-2-15(10(5)14-4-13-9)11-8(18)7(17)6(3-16)19-11/h1-2,4,6-8,11,16-18H,3H2,(H2,12,13,14)/t6-,7-,8-,11-/m1/s1
InChI Key HDZZVAMISRMYHH-KCGFPETGSA-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/)
References
1. Anzai K, Nakamura G, Suzuki S. (1957)
A new antibiotic, tubercidin.
J Antibiot (Tokyo), 10 (5): 201-4. DOI: 10.11554/antibioticsa.10.5_201 [PMID:13513512]
2. Baldwin SA, Yao SY, Hyde RJ, Ng AM, Foppolo S, Barnes K, Ritzel MW, Cass CE, Young JD. (2005)
Functional characterization of novel human and mouse equilibrative nucleoside transporters (hENT3 and mENT3) located in intracellular membranes.
J Biol Chem, 280 (16): 15880-7. [PMID:15701636]
3. Bisel HF, Ansfield FJ, Mason JH, Wilson WL. (1970)
Clinical studies with tubercidin administered by direct intravenous injection.
Cancer Res, 30 (1): 76-8. [PMID:4917978]
4. Grage TB, Rochlin DB, Weiss AJ, Wilson WL. (1970)
Clinical studies with tubercidin administered after absorption into human erythrocytes.
Cancer Res, 30 (1): 79-81. [PMID:4985935]
5. Sun Q, Liao X, Yan J, Jiang G, Huo F, Wang G, Li H. (2023)
In vitro activity of tubercidin against Mycobacterium tuberculosis and nontuberculosis Mycobacteria.
J Med Microbiol, 72 (11). [PMID:37910006]