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herbimycin A   Click here for help

GtoPdb Ligand ID: 5984

Compound class: Natural product
Comment: Herbimycin A is a Streptomyces-derived cell-permeable inhibitor of non-receptor tyrosine kinases [2,4,6].
As with other natural products, there is ambiguity in the precise stereochemisrty presented across web resources eg PubChem CID 6436247 shows an alternate structure.
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 11
Hydrogen bond donors 2
Rotatable bonds 6
Topological polar surface area 152.48
Molecular weight 574.29
XLogP 0.84
No. Lipinski's rules broken 1

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 COC1C(C)C=C(C)C(OC(=O)N)C(OC)C=CC=C(C(=O)NC2=CC(=O)C=C(C(C(CC1OC)C)OC)C2=O)C
Isomeric SMILES COC1[C@@H](C)/C=C(\C)/[C@H](OC(=O)N)C(OC)/C=C\C=C(\C(=O)NC2=CC(=O)C=C([C@@H]([C@H](C[C@@H]1OC)C)OC)C2=O)/C
InChI InChI=1S/C30H42N2O9/c1-16-10-9-11-23(37-5)28(41-30(31)36)18(3)12-17(2)27(40-8)24(38-6)13-19(4)26(39-7)21-14-20(33)15-22(25(21)34)32-29(16)35/h9-12,14-15,17,19,23-24,26-28H,13H2,1-8H3,(H2,31,36)(H,32,35)/b11-9-,16-10+,18-12+/t17-,19-,23?,24-,26+,27?,28-/m0/s1
InChI Key MCAHMSDENAOJFZ-NDSMKMDISA-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/)

Large-scale screening data

EMD Millipore KinaseProfilerTM screen/Reaction Biology Kinase HotspotSM screen Click here for help
A screen profiling 158 kinase inhibitors (Calbiochem Protein Kinase Inhibitor Library I and II, catalogue numbers 539744 and 539745) for their inhibitory activity at 1µM and 10µM against 234 human recombinant kinases using the EMD Millipore KinaseProfilerTM service.

A screen profiling the inhibitory activity of 178 commercially available kinase inhibitors at 0.5µM against a panel of 300 recombinant protein kinases using the Reaction Biology Corporation Kinase HotspotSM platform.

http://www.millipore.com/techpublications/tech1/pf3036
http://www.reactionbiology.com/webapps/main/pages/kinase.aspx

Reference: 1,3
Key to terms and symbols Click column headers to sort
Target Name in screen Sp. Type Action % Activity remaining at 0.5µM % Activity remaining at 1µM % Activity remaining at 10µM
mitogen-activated protein kinase kinase kinase 14 nd/NIK(MAP3K14) Hs Inhibitor Inhibition 67.9
interleukin 1 receptor associated kinase 1 IRAK1/IRAK1 Hs Inhibitor Inhibition 71.8 106.0 94.0
ribosomal protein S6 kinase A1 Rsk1/RSK1 Hs Inhibitor Inhibition 76.8 115.0 84.0
cyclin dependent kinase 1 CDK1-cyclin B/CDK1-cyclin B Hs Inhibitor Inhibition 77.5 111.0 110.0
serine/threonine kinase 24 MST3/MST3(STK24) Hs Inhibitor Inhibition 79.6 68.0 72.0
serine/threonine-protein kinase MST4 nd/MSTR4 Hs Inhibitor Inhibition 85.3
casein kinase 1 epsilon nd/CK1epsilon Hs Inhibitor Inhibition 85.9
serine/threonine kinase 39 nd/STK39(STLK3) Hs Inhibitor Inhibition 86.5
protein kinase C zeta PKCζ/PKCzeta Hs Inhibitor Inhibition 86.8 104.0 106.0
CDC like kinase 4 nd/CLK4 Hs Inhibitor Inhibition 86.9
Displaying the top 10 targets  View all targets in screen »