SU9516   Click here for help

GtoPdb Ligand ID: 6045

Synonyms: AC1NRD9P | SU-9516
PDB Ligand
Compound class: Synthetic organic
Comment: SU9516 is a potent inhibitor of several cyclin-dependent kinases (CDKs) with reported selectivity for CDK2 [4]. Later analysis of SU9516's selectivity profile indicates a similar level of potency as an inhibitor of CDK5/p25 compared to CDK2 [3]. Inhibition of CDK5 was confirmed in a cellular assay measuring dephosphorylation of pFAK(S732). SU9516 also arrests cells at the G2/M phase in cells lacking CDK2, in which case it must be causing the cell cycle arrest via inhibition of CDK1 [3].
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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

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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 3
Hydrogen bond donors 2
Rotatable bonds 2
Topological polar surface area 67.01
Molecular weight 241.09
XLogP 0.97
No. Lipinski's rules broken 0
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 COc1ccc2c(c1)C(=Cc1cnc[nH]1)C(=O)N2
Isomeric SMILES COc1ccc2c(c1)/C(=C/c1cnc[nH]1)/C(=O)N2
InChI InChI=1S/C13H11N3O2/c1-18-9-2-3-12-10(5-9)11(13(17)16-12)4-8-6-14-7-15-8/h2-7H,1H3,(H,14,15)(H,16,17)/b11-4-
InChI Key QNUKRWAIZMBVCU-WCIBSUBMSA-N
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
(3Z)-3-(1H-imidazol-5-ylmethylidene)-5-methoxy-2,3-dihydro-1H-indol-2-one
Synonyms Click here for help
AC1NRD9P | SU-9516
Database Links Click here for help
CAS Registry No. 666837-93-0
ChEMBL Ligand CHEMBL258805
DrugBank Ligand DB03428
GtoPdb PubChem SID 178102667
PubChem CID 5289419
RCSB PDB Ligand SU9
Search Google for chemical match using the InChIKey QNUKRWAIZMBVCU-WCIBSUBMSA-N
Search Google for chemicals with the same backbone QNUKRWAIZMBVCU
SynPHARM 80574 (in complex with cyclin dependent kinase 2)
85576 (in complex with cyclin dependent kinase 2)
85577 (in complex with cyclin dependent kinase 2)
UniChem Compound Search for chemical match using the InChIKey QNUKRWAIZMBVCU-WCIBSUBMSA-N
UniChem Connectivity Search for chemical match using the InChIKey QNUKRWAIZMBVCU-WCIBSUBMSA-N

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Tocris
SU 9516 (links to external site)
Cat. No. 2907