PFI-4   Click here for help

GtoPdb Ligand ID: 8575

PDB Ligand
Compound class: Synthetic organic
Comment: This compound from the Structural Genomics Consortium's (SGC) Epigenetics Probes Collection, is a useful tool for studying the function of the bromodomain-containing protein, BRPF1. BRPF proteins 1, 2 and 3 provide the scaffold for the formation of MYST complexes which play essential functions in DNA repair, recombination, replication and activation of transcription. PFI-4 is selective for the BRPF1B isoform. The BRPF1A isoform contains an amino acid insertion which prevents its binding to acetylated histone peptides.
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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 4
Hydrogen bond donors 1
Rotatable bonds 5
Topological polar surface area 68.5
Molecular weight 380.18
XLogP 2.46
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 COc1ccccc1C(=O)Nc1cc2c(cc1N1CCCC1)n(c(=O)n2C)C
Isomeric SMILES COc1ccccc1C(=O)Nc1cc2c(cc1N1CCCC1)n(c(=O)n2C)C
InChI InChI=1S/C21H24N4O3/c1-23-17-12-15(22-20(26)14-8-4-5-9-19(14)28-3)16(25-10-6-7-11-25)13-18(17)24(2)21(23)27/h4-5,8-9,12-13H,6-7,10-11H2,1-3H3,(H,22,26)
InChI Key QCIJLRJBZDBVDB-UHFFFAOYSA-N
Classification Click here for help
Compound class Synthetic organic
IUPAC Name Click here for help
N-(1,3-dimethyl-2-oxo-6-pyrrolidin-1-ylbenzimidazol-5-yl)-2-methoxybenzamide
Database Links Click here for help
GtoPdb PubChem SID 252166776
PubChem CID 40642506
RCSB PDB Ligand 5XF
Search Google for chemical match using the InChIKey QCIJLRJBZDBVDB-UHFFFAOYSA-N
Search Google for chemicals with the same backbone QCIJLRJBZDBVDB
SynPHARM 82372 (in complex with bromodomain and PHD finger containing 1)
UniChem Compound Search for chemical match using the InChIKey QCIJLRJBZDBVDB-UHFFFAOYSA-N
UniChem Connectivity Search for chemical match using the InChIKey QCIJLRJBZDBVDB-UHFFFAOYSA-N

Product suppliers

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Product supplier links are provided as a service to assist in identifying commercial suppliers of reagents that are mentioned on the IUPHAR/BPS Guide to PHARMACOLOGY database website, and do not imply their endorsement by NC-IUPHAR.

Links are provided in return for sponsorship, used to fund improvements to this database. The sponsorship account is managed and audited by the University of Edinburgh, a charitable body registered in Scotland, SC005336. If you are interested in sponsoring the database, please contact us.

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Tocris
PFI 4 (links to external site)
Cat. No. 5576