ginkgolide B   Click here for help

GtoPdb Ligand ID: 1862

Abbreviated name: GKB
Synonyms: BN 52021
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.
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2D Structure
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Physico-chemical Properties
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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
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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
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]