ibogaine   Click here for help

GtoPdb Ligand ID: 13148

Synonyms: (-)-Ibogaine | (5β)-12-methoxyibogamine | 12-Methoxyibogamine
PDB Ligand
Compound class: Natural product
Comment: Ibogaine is a naturally occurring dissociative psychoactive substance found in plants of the Apocynaceae (dogbane) family. It is one of the so-called iboga alkaloids (ibogaine, noribogaine, voacangine, coronaridine, ibogaline and tabernanthine) [3]. Cryo-EM studies have shown ibogaine bound to the human serotonin transporter (SERT; SLC6A4) [1].
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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.

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View interactive charts of activity data across species
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 3
Hydrogen bond donors 1
Rotatable bonds 2
Topological polar surface area 24.5
Molecular weight 310.43
XLogP 2.83
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 CC[C@H]1C[C@@H]2C[C@H]3C4=C(CCN(C2)[C@@H]13)C5=C(C=CC(=C5)OC)N4
Isomeric SMILES CC[C@H]1C[C@@H]2C[C@@H]3[C@H]1N(C2)CCC4=C3NC5=C4C=C(C=C5)OC
InChI InChI=1S/C20H26N2O/c1-3-13-8-12-9-17-19-15(6-7-22(11-12)20(13)17)16-10-14(23-2)4-5-18(16)21-19/h4-5,10,12-13,17,20-21H,3,6-9,11H2,1-2H3/t12-,13+,17+,20+/m1/s1
InChI Key HSIBGVUMFOSJPD-CFDPKNGZSA-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/)
References
1. Coleman JA, Yang D, Zhao Z, Wen PC, Yoshioka C, Tajkhorshid E, Gouaux E. (2019)
Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport.
Nature, 569 (7754): 141-145. [PMID:31019304]
2. Glick SD, Maisonneuve IM, Szumlinski KK. (2001)
Mechanisms of action of ibogaine: relevance to putative therapeutic effects and development of a safer iboga alkaloid congener.
Alkaloids Chem Biol, 56: 39-53. [PMID:11705115]
3. Iyer RN, Favela D, Zhang G, Olson DE. (2021)
The iboga enigma: the chemistry and neuropharmacology of iboga alkaloids and related analogs.
Nat Prod Rep, 38 (2): 307-329. [PMID:32794540]
4. Kargbo RB. (2022)
Ibogaine and Their Analogs as Therapeutics for Neurological and Psychiatric Disorders.
ACS Med Chem Lett, 13 (6): 888-890. [PMID:35707155]
5. Litjens RP, Brunt TM. (2016)
How toxic is ibogaine?.
Clin Toxicol (Phila), 54 (4): 297-302. [PMID:26807959]
6. Sun YT, Wang GF, Yang YQ, Jin F, Wang Y, Xie XY, Mach RH, Huang YS. (2018)
Synthesis and pharmacological evaluation of 6,7-dimethoxy-1,2,3,4-tetrahydroisoquinoline derivatives as sigma-2 receptor ligands.
Eur J Med Chem, 147: 227-237. [PMID:29438891]