mycoplanecin A   Click here for help

GtoPdb Ligand ID: 13757

Compound class: Natural product
Comment: Mycoplanecin A is a natural product from Actinoplanes awajinensis subsp. mycoplanecinus that has potent antimycobacterial activity [2-4]. Functionally, it is an inhibitor of Mycobacterium beta sliding clamp (DnaN) [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 23
Hydrogen bond donors 3
Rotatable bonds 19
Topological polar surface area 272.84
Molecular weight 1183.52
XLogP 6.31
No. Lipinski's rules broken 4

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 CCC1CC(C(=O)N(C)C2C(C)OC(=O)CNC(=O)C(CC(C)C)N(C)C(=O)C3CCCN3C(=O)C(C(C)C)N(C)C(=O)C(CCC(C)C)NC(=O)C4CC(C)CN4C(=O)C(CC(C)C)NC2=O)N(C1)C(=O)C(C(C)C)N(C)C(=O)C(=O)CC
Isomeric SMILES CCC1CC(N(C1)C(=O)C(C(C)C)N(C)C(=O)C(=O)CC)C(=O)N(C)C2C(OC(=O)CNC(=O)C(N(C(=O)C3CCCN3C(=O)C(N(C(=O)C(NC(=O)C4CC(CN4C(=O)C(NC2=O)CC(C)C)C)CCC(C)C)C)C(C)C)C)CC(C)C)C
InChI InChI=1S/C61H102N10O13/c1-19-40-29-46(71(32-40)61(83)50(37(11)12)67(17)59(81)47(72)20-2)58(80)68(18)51-39(14)84-48(73)30-62-52(74)44(27-35(7)8)65(15)57(79)43-22-21-25-69(43)60(82)49(36(9)10)66(16)55(77)41(24-23-33(3)4)63-53(75)45-28-38(13)31-70(45)56(78)42(26-34(5)6)64-54(51)76/h33-46,49-51H,19-32H2,1-18H3,(H,62,74)(H,63,75)(H,64,76)
InChI Key ICFLLAYTOVAMGO-UHFFFAOYSA-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
Mycoplanecin A demonstrates antibacterial activity in vitro that is primarily against Mycobacterium spp. and closely related bacteria [2]. The MIC for in vitro antimycobacterial activity against M. tuberculosis H37Rv is 0.102 μg/ml and 0.0625 μg/ml against M. smegmatis [1].
Mycoplanecin A binds M. smegmatis DnaN with a dissociation constant (Kd) of 95 nM [1].