CDK12 inhibitor 2   Click here for help

GtoPdb Ligand ID: 10063

Compound class: Synthetic organic
Comment: This compound is a novel and selective cyclin-dependent kinase 12 (CDK12) and CDK13 inhibitor [1]. It is a chemical probe that is suitable for functional studies of CDK12, and a scaffold for further drug discovery efforts. CDK12 is an oncology drug target as its inhibition sensitises cancer cells to DNA-damaging reagents and DNA-repair inhibitors. The chemical structure was generated from the SMILES string supplied with the original J Med Chem article by Ito et al. (2018) [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 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.

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Hydrogen bond acceptors 7
Hydrogen bond donors 2
Rotatable bonds 9
Topological polar surface area 103.05
Molecular weight 532.26
XLogP 6.16
No. Lipinski's rules broken 1
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.

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Canonical SMILES N#Cc1ccc(nc1)NC1CCC(CC1)N(c1ccc(cc1)c1ccc(=O)n(c1)C)C(=O)NCc1ccccc1
Isomeric SMILES N#Cc1ccc(nc1)N[C@@H]1CC[C@H](CC1)N(c1ccc(cc1)c1ccc(=O)n(c1)C)C(=O)NCc1ccccc1
InChI InChI=1S/C32H32N6O2/c1-37-22-26(10-18-31(37)39)25-8-13-28(14-9-25)38(32(40)35-20-23-5-3-2-4-6-23)29-15-11-27(12-16-29)36-30-17-7-24(19-33)21-34-30/h2-10,13-14,17-18,21-22,27,29H,11-12,15-16,20H2,1H3,(H,34,36)(H,35,40)/t27-,29-
InChI Key HDJBGURZVALLMD-KWQFAZJVSA-N
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
3-Benzyl-1-(trans-4-((5-cyanopyridin-2-yl)amino)cyclohexyl)-1-(4-(1-methyl-6-oxo-1,6-dihydropyridin-3-yl)phenyl)urea
Database Links Click here for help
GtoPdb PubChem SID 375973251
PubChem CID 134813906
Search Google for chemical match using the InChIKey HDJBGURZVALLMD-KWQFAZJVSA-N
Search Google for chemicals with the same backbone HDJBGURZVALLMD
UniChem Compound Search for chemical match using the InChIKey HDJBGURZVALLMD-KWQFAZJVSA-N
UniChem Connectivity Search for chemical match using the InChIKey HDJBGURZVALLMD-KWQFAZJVSA-N