LP99   Click here for help

GtoPdb Ligand ID: 8572

Synonyms: compound 60 [PMID: 25864491]
PDB Ligand
Compound class: Synthetic organic
Comment: LP99 is a selective inhibitor of the bromodomain-containing proteins BRD7 and BRD9 [1], proteins which participate in chromatin remodelling as part of the SWI/SNF complex. LP99 is a novel and useful chemical probe for investigating BRD7/9 function. This is a compound from the Structural Genomics Consortium's (SGC) Epigenetics Probes Collection.
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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

LP99 is commercially available from our sponsors

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 6
Hydrogen bond donors 1
Rotatable bonds 6
Topological polar surface area 96.86
Molecular weight 515.16
XLogP 5.38
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 Clc1ccc(cc1)C1C(CCC(=O)N1c1ccc2c(c1)n(C)c(=O)cc2C)NS(=O)(=O)CC(C)C
Isomeric SMILES Clc1ccc(cc1)[C@@H]1[C@H](CCC(=O)N1c1ccc2c(c1)n(C)c(=O)cc2C)NS(=O)(=O)CC(C)C
InChI InChI=1S/C26H30ClN3O4S/c1-16(2)15-35(33,34)28-22-11-12-24(31)30(26(22)18-5-7-19(27)8-6-18)20-9-10-21-17(3)13-25(32)29(4)23(21)14-20/h5-10,13-14,16,22,26,28H,11-12,15H2,1-4H3/t22-,26+/m0/s1
InChI Key LVDRREOUMKACNJ-BKMJKUGQSA-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/)
Bioactivity Comments
The activity of LP99 is stereo-specific. The alternative (2S, 3R)-LP99 isomer does not bind BRD9 [1]. In vitro experiments using LPS-activated THP-1 monocytes show that BRD7/9 plays a role in regulating pro-inflammatory cytokine secretion [1].
Selectivity at enzymes
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
bromodomain containing 9 Primary target of this compound Hs Inhibitor Inhibition 7.0 pKd - 1
⤷ pKd 7.0 (Kd 9.9x10-8 M) [1]
Description: Isothermal titration calorimetry (ITC) assay
bromodomain containing 7 Hs Inhibitor Inhibition ~6.0 pKd - 1
⤷ pKd ~6.0 (Kd ~1x10-6 M) [1]
Description: Based on binding of BRD7 being 10-fold lower than for BRD9