ginkgolide B   Click here for help

GtoPdb Ligand ID: 1862

Abbreviated name: GKB
Synonyms: BN 52021
Compound class: Natural product or derivative
Comment: From the plant Ginkgo biloba. There is some ambiguity on online resources as to the exact stereochemistry of ginkgolide B. Other representations on PubChem include CID 11973122 and CID 6917929.
Click here for help

Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

✖

View interactive charts of activity data across species
2D Structure
Click here for help

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.

✖
Click here for structure editor
Physico-chemical Properties
Click here for help

Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. 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.

✖
Hydrogen bond acceptors 10
Hydrogen bond donors 3
Rotatable bonds 1
Topological polar surface area 148.82
Molecular weight 424.14
XLogP 0.15
No. Lipinski's rules broken 0
SMILES / InChI / InChIKey
Click here for help

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.

✖
Canonical SMILES O=C1OC2C(C1C)(O)C13C4(C2O)C(OC3=O)CC(C24C(O1)OC(=O)C2O)C(C)(C)C
Isomeric SMILES O=C1O[C@@H]2[C@@]([C@@H]1C)(O)[C@@]13C4(C2O)[C@H](OC3=O)C[C@H](C24[C@H](O1)OC(=O)C2O)C(C)(C)C
InChI InChI=1S/C20H24O10/c1-6-12(23)28-11-9(21)18-8-5-7(16(2,3)4)17(18)10(22)13(24)29-15(17)30-20(18,14(25)27-8)19(6,11)26/h6-11,15,21-22,26H,5H2,1-4H3/t6-,7+,8-,9?,10?,11+,15+,17?,18?,19-,20-/m1/s1
InChI Key SQOJOAFXDQDRGF-OOHPMXMZSA-N
References
1. Hawthorne R, Cromer BA, Ng HL, Parker MW, Lynch JW. (2006)
Molecular determinants of ginkgolide binding in the glycine receptor pore.
J Neurochem, 98 (2): 395-407. [PMID:16805834]
2. Heads JA, Hawthorne RL, Lynagh T, Lynch JW. (2008)
Structure-activity analysis of ginkgolide binding in the glycine receptor pore.
J Neurochem, 105 (4): 1418-27. [PMID:18221374]
3. Strømgaard K, Saito DR, Shindou H, Ishii S, Shimizu T, Nakanishi K. (2002)
Ginkgolide derivatives for photolabeling studies: preparation and pharmacological evaluation.
J Med Chem, 45 (18): 4038-46. [PMID:12190325]
4. Thompson AJ, Duke RK, Lummis SC. (2011)
Binding sites for bilobalide, diltiazem, ginkgolide, and picrotoxinin at the 5-HT3 receptor.
Mol Pharmacol, 80 (1): 183-90. [PMID:21505038]
5. Thompson AJ, Jarvis GE, Duke RK, Johnston GA, Lummis SC. (2011)
Ginkgolide B and bilobalide block the pore of the 5-HT(3) receptor at a location that overlaps the picrotoxin binding site.
Neuropharmacology, 60 (2-3): 488-95. [PMID:21059362]
6. Vogensen SB, Stromgaard K, Shindou H, Jaracz S, Suehiro M, Ishii S, Shimizu T, Nakanishi K. (2003)
Preparation of 7-substituted ginkgolide derivatives: potent platelet activating factor (PAF) receptor antagonists.
J Med Chem, 46: 601-608. [PMID:12570381]