SIM1   Click here for help

GtoPdb Ligand ID: 11777

Synonyms: compound 3 [PMID: 34675414]
Compound class: Synthetic organic
Comment: SIM1 is a first-in-class trivalent PROTAC molecule [1]. It contains two bromo and extra terminal (BET) domain inhibitor ligand components and a von Hippel-Lindau (VHL) ligand domain which are tethered together by a branched linker. This approach increases the valency for target protein binding compared to earlier generation bivalent PROTAC molecules. SIM1 acts as a low picomolar BET degrader in vitro, and has favourable in vivo pharmacokinetics. BET inhibitors are being explored for anticancer activity.
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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

SIM1 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 25
Hydrogen bond donors 5
Rotatable bonds 44
Topological polar surface area 404.26
Molecular weight 1616.6
XLogP 9.47
No. Lipinski's rules broken 3

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)C1=N[C@@H](CC(=O)NCCOCCOCCOCC(COCC(=O)N[C@@H](C(C)(C)C)C(=O)N2C[C@@H](C[C@H]2C(=O)NCc2ccc(cc2)c2scnc2C)O)(COCCOCCOCCNC(=O)C[C@@H]2N=C(c3ccc(cc3)Cl)c3c(n4c2nnc4C)sc(c3C)C)C)c2n(c3c1c(C)c(s3)C)c(nn2)C
Isomeric SMILES O[C@@H]1C[C@H](N(C1)C(=O)[C@H](C(C)(C)C)NC(=O)COCC(COCCOCCOCCNC(=O)C[C@H]1c2n(c3c(C(=N1)c1ccc(cc1)Cl)c(c(s3)C)C)c(nn2)C)(COCCOCCOCCNC(=O)C[C@H]1c2n(c3c(C(=N1)c1ccc(cc1)Cl)c(c(s3)C)C)c(nn2)C)C)C(=O)NCc1ccc(cc1)c1c(ncs1)C
InChI InChI=1S/C79H98Cl2N14O13S3/c1-46-49(4)110-76-66(46)68(54-16-20-57(80)21-17-54)86-60(72-91-89-51(6)94(72)76)37-63(97)82-24-26-102-28-30-104-32-34-106-42-79(11,44-108-41-65(99)88-71(78(8,9)10)75(101)93-40-59(96)36-62(93)74(100)84-39-53-12-14-56(15-13-53)70-48(3)85-45-109-70)43-107-35-33-105-31-29-103-27-25-83-64(98)38-61-73-92-90-52(7)95(73)77-67(47(2)50(5)111-77)69(87-61)55-18-22-58(81)23-19-55/h12-23,45,59-62,71,96H,24-44H2,1-11H3,(H,82,97)(H,83,98)(H,84,100)(H,88,99)/t59-,60+,61+,62+,71-/m1/s1
InChI Key RARNTROXRCXFHV-CMRSQZKGSA-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
SIM1 binds to immobilised VHL with a Kd of 624 nM [1]. The binding affinity of SIM1/BRD2 complexes for VHL is higher at ~40 nM.In vitroSIM1 degrades BRD2 with a DC50 value of 1.1 nM, and reduces viability of MV4;11 AML cells with an IC50 of 1.1 nM.
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 2 Hs Inhibitor Binding 10.5 pKd - 1
⤷ pKd 10.5 (Kd 3.3x10-11 M) [1]
Description: Binding affinity for BRD2(1,2) by BROMOscan assay