SMD-3040   Click here for help

GtoPdb Ligand ID: 12842

Synonyms: compound 29 [PMID: 37523716] | SMD3040
Compound class: Synthetic organic
Comment: SMD-3040 is an experimental SMARCA2 PROTAC degrader [1]. It uses a SMARCA2/4 bromodomain-binding ligand (SMARCA2/4 ligand 3 [1]) to recruit the target protein to the VHL E3 ligase to initiate its proteasomal degradation. Targeting SMARCA2 in SMARCA4 deficient tumours induces synthetic lethality in preclinical tumour models.
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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 15
Hydrogen bond donors 5
Rotatable bonds 16
Topological polar surface area 226.21
Molecular weight 943.21
XLogP 4.85
No. Lipinski's rules broken 3
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 C[C@@H](C1=CC=C(C=C1)C2=C(C)N=CS2)NC(=O)[C@@H]3C[C@H](CN3C(=O)[C@H](C(C)(C)C)NC(=O)[C@H]4CC[C@@H](CC4)CN5CC6(CCC(CC6)N7C=C(C=N7)C8=C(N)N=NC(=C8)C9=C(C=CC=C9)O)C5)O
Isomeric SMILES NC1=C(C2=CN(C3CCC4(CN(C[C@H]5CC[C@@H](CC5)C(N[C@@H](C(C)(C)C)C(N6[C@H](C(N[C@@H](C)C7=CC=C(C8=C(C)N=CS8)C=C7)=O)C[C@@H](O)C6)=O)=O)C4)CC3)N=C2)C=C(C9=C(O)C=CC=C9)N=N1
InChI InChI=1S/C52H66N10O5S/c1-31(34-14-16-35(17-15-34)45-32(2)54-30-68-45)56-49(66)43-22-39(63)27-61(43)50(67)46(51(3,4)5)57-48(65)36-12-10-33(11-13-36)25-60-28-52(29-60)20-18-38(19-21-52)62-26-37(24-55-62)41-23-42(58-59-47(41)53)40-8-6-7-9-44(40)64/h6-9,14-17,23-24,26,30-31,33,36,38-39,43,46,63-64H,10-13,18-22,25,27-29H2,1-5H3,(H2,53,59)(H,56,66)(H,57,65)/t31-,33-,36-,39+,43-,46+/m0/s1
InChI Key GMCWCUOAGNWNLO-YTZIVEPUSA-N
Bioactivity Comments
DC50 for SMARCA2 is 12 nM [1]. Although SMD-3040's SMARCA-binding moiety has similar affinities for both SMARCA2 and SMARCA4 it achieves a higher maximum degradation of SMARCA2 (>90%) over SMARCA4 (~50%).
Selectivity at other protein targets
Key to terms and symbols Click column headers to sort
Target Sp. Type Action Value Parameter Concentration range (M) Reference
SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 Hs None Binding 8.0 pKd - 1
⤷ pKd 8.0 (Kd 1x10-8 M) [1]
Description: Binding affinity of SMARCA2/4 ligand 3 moiety
SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 Hs None Binding 7.9 pKd - 1
⤷ pKd 7.9 (Kd 1.28x10-8 M) [1]
Description: Binding affinity of SMARCA2/4 ligand 3 moiety