vanillobiocin   Click here for help

GtoPdb Ligand ID: 12130

Synonyms: novclobiocin 311
Compound class: Natural product
Comment: Vanillobiocin is an aminocoumarin antibacterial compound isolated from the culture broth of a cloQ- mutant of the clorobiocin producer Streptomyces roseochromogenes [1]. The same study also identified isovanillobiocin and declovanillobiocin.
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 5
Rotatable bonds 10
Topological polar surface area 199.01
Molecular weight 658.16
XLogP 4.51
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 CO[C@@H]1[C@@H](OC(=O)c2ccc([nH]2)C)[C@@H](O)[C@@H](OC1(C)C)Oc1ccc2c(c1Cl)oc(=O)c(c2O)NC(=O)c1ccc(c(c1)OC)O
Isomeric SMILES Cc1ccc([nH]1)C(=O)O[C@H]1[C@H]([C@@H](OC([C@@H]1OC)(C)C)Oc1c(c2c(cc1)c(c(c(=O)o2)NC(=O)c1cc(c(cc1)O)OC)O)Cl)O
InChI InChI=1S/C31H31ClN2O12/c1-13-6-9-16(33-13)28(39)45-25-23(37)30(46-31(2,3)26(25)42-5)43-18-11-8-15-22(36)21(29(40)44-24(15)20(18)32)34-27(38)14-7-10-17(35)19(12-14)41-4/h6-12,23,25-26,30,33,35-37H,1-5H3,(H,34,38)/t23-,25+,26-,30-/m1/s1
InChI Key LNDDBMXOCFEELJ-CPPKFOPJSA-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/)
Classification Click here for help
Compound class Natural product
IUPAC Name Click here for help
[(3R,4S,5R,6S)-6-[8-chloro-4-hydroxy-3-[(4-hydroxy-3-methoxybenzoyl)amino]-2-oxochromen-7-yl]oxy-5-hydroxy-3-methoxy-2,2-dimethyloxan-4-yl] 5-methyl-1H-pyrrole-2-carboxylate
Synonyms Click here for help
novclobiocin 311
Database Links Click here for help
Specialist databases
Antibiotic DB Antibiotic DB Database logo Vanillobiocin
Other databases
CAS Registry No. 744218-18-6 (source: Scifinder)
ChEMBL Ligand CHEMBL1275884
GtoPdb PubChem SID 472319252
PubChem CID 54708659
Search Google for chemical match using the InChIKey LNDDBMXOCFEELJ-CPPKFOPJSA-N
Search Google for chemicals with the same backbone LNDDBMXOCFEELJ
UniChem Compound Search for chemical match using the InChIKey LNDDBMXOCFEELJ-CPPKFOPJSA-N
UniChem Connectivity Search for chemical match using the InChIKey LNDDBMXOCFEELJ-CPPKFOPJSA-N