NCL-1   Click here for help

GtoPdb Ligand ID: 7024

Compound class: Synthetic organic
Comment: This is the 1S, 2R optical isomer of NCL-1. This isomer is more biologically active than the 1R, 2S isomer [2].

Histone demethylation by KDM1A is suggested to be associated with some cancers and herpes simplex infection [1,3]. So, KDM1A inhibitors are of interest both as investigational tools and potential disease modifiers.
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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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Click here for structure editor
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 5
Hydrogen bond donors 3
Rotatable bonds 12
Topological polar surface area 93.45
Molecular weight 443.22
XLogP 3.83
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 O=C(C(NC(=O)c1ccccc1)CCOc1cccc(c1)C1CC1N)NCc1ccccc1
Isomeric SMILES O=C([C@H](NC(=O)c1ccccc1)CCOc1cccc(c1)[C@@H]1C[C@H]1N)NCc1ccccc1
InChI InChI=1S/C27H29N3O3/c28-24-17-23(24)21-12-7-13-22(16-21)33-15-14-25(30-26(31)20-10-5-2-6-11-20)27(32)29-18-19-8-3-1-4-9-19/h1-13,16,23-25H,14-15,17-18,28H2,(H,29,32)(H,30,31)/t23-,24+,25+/m0/s1
InChI Key DTPSXFMGMQOVTG-ISJGIBHGSA-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. Liang Y, Vogel JL, Narayanan A, Peng H, Kristie TM. (2009)
Inhibition of the histone demethylase LSD1 blocks alpha-herpesvirus lytic replication and reactivation from latency.
Nat Med, 15 (11): 1312-7. [PMID:19855399]
2. Ogasawara D, Suzuki T, Mino K, Ueda R, Khan MN, Matsubara T, Koseki K, Hasegawa M, Sasaki R, Nakagawa H et al.. (2011)
Synthesis and biological activity of optically active NCL-1, a lysine-specific demethylase 1 selective inhibitor.
Bioorg Med Chem, 19 (12): 3702-8. [PMID:21227703]
3. Schulte JH, Lim S, Schramm A, Friedrichs N, Koster J, Versteeg R, Ora I, Pajtler K, Klein-Hitpass L, Kuhfittig-Kulle S et al.. (2009)
Lysine-specific demethylase 1 is strongly expressed in poorly differentiated neuroblastoma: implications for therapy.
Cancer Res, 69 (5): 2065-71. [PMID:19223552]