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dBET57

Alias: dBET57 dBET-57 dBET 57
Cat No.:V19243 Purity: ≥98%
dBET57 is a novel BRD4 heterobifunctional small-molecule ligand (PROTAC) which exhibits significant and selective degradation of BRD4 BD1 but is inactive on BRD4 BD2.
dBET57
dBET57 Chemical Structure CAS No.: 1883863-52-2
Product category: Epigenetic Reader Domain
This product is for research use only, not for human use. We do not sell to patients.
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Purity & Quality Control Documentation

Purity: ≥98%

Product Description

dBET57 is a novel BRD4 heterobifunctional small-molecule ligand (PROTAC) which exhibits significant and selective degradation of BRD4 BD1 but is inactive on BRD4 BD2.

Physicochemical Properties
Molecular Formula
C34H31CLN8O5S
Molecular Weight
699.18
Exact Mass
698.1827
CAS #
1883863-52-2
Related CAS #
1883863-52-2
Appearance
Typically exists as solids (or liquids in special cases) at room temperature
SMILES
O=C(NCCNC1=CC=CC(C(N2C(CC3)C(NC3=O)=O)=O)=C1C2=O)C[C@H]4C5=NN=C(C)N5C6=C(C(C)=C(C)S6)C(C7=CC=C(Cl)C=C7)=N4
InChi Key
CZRLOIDJCMKJHE-UXMRNZNESA-N
InChi Code
InChI=1S/C34H31ClN8O5S/c1-16-17(2)49-34-27(16)29(19-7-9-20(35)10-8-19)38-23(30-41-40-18(3)42(30)34)15-26(45)37-14-13-36-22-6-4-5-21-28(22)33(48)43(32(21)47)24-11-12-25(44)39-31(24)46/h4-10,23-24,36H,11-15H2,1-3H3,(H,37,45)(H,39,44,46)/t23-,24?/m0/s1
Chemical Name
2-((S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl)-N-(2-((2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-4-yl)amino)ethyl)acetamide
Synonyms
dBET57 dBET-57 dBET 57
HS Tariff Code
2934.99.9001
Storage

Powder      -20°C    3 years

                     4°C     2 years

In solvent   -80°C    6 months

                  -20°C    1 month

Note: This product requires protection from light (avoid light exposure) during transportation and storage.
Shipping Condition
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
Solubility Data
Solubility (In Vitro)
DMSO : ~250 mg/mL (~357.56 mM)
Solubility (In Vivo)
Solubility in Formulation 1: ≥ 2.08 mg/mL (2.97 mM) (saturation unknown) in 10% DMSO + 40% PEG300 +5% Tween-80 + 45% Saline (add these co-solvents sequentially from left to right, and one by one), clear solution.
For example, if 1 mL of working solution is to be prepared, you can add 100 μL of 20.8 mg/mL clear DMSO stock solution to 400 μL PEG300 and mix evenly; then add 50 μL Tween-80 + to the above solution and mix evenly; then add 450 μL normal saline to adjust the volume to 1 mL.
Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH₂ O to obtain a clear solution.

 (Please use freshly prepared in vivo formulations for optimal results.)
Preparing Stock Solutions 1 mg 5 mg 10 mg
1 mM 1.4302 mL 7.1512 mL 14.3025 mL
5 mM 0.2860 mL 1.4302 mL 2.8605 mL
10 mM 0.1430 mL 0.7151 mL 1.4302 mL

*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.

Calculator

Molarity Calculator allows you to calculate the mass, volume, and/or concentration required for a solution, as detailed below:

  • Calculate the Mass of a compound required to prepare a solution of known volume and concentration
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An example of molarity calculation using the molarity calculator is shown below:
What is the mass of compound required to make a 10 mM stock solution in 5 ml of DMSO given that the molecular weight of the compound is 350.26 g/mol?
  • Enter 350.26 in the Molecular Weight (MW) box
  • Enter 10 in the Concentration box and choose the correct unit (mM)
  • Enter 5 in the Volume box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 17.513 mg appears in the Mass box. In a similar way, you may calculate the volume and concentration.

Dilution Calculator allows you to calculate how to dilute a stock solution of known concentrations. For example, you may Enter C1, C2 & V2 to calculate V1, as detailed below:

What volume of a given 10 mM stock solution is required to make 25 ml of a 25 μM solution?
Using the equation C1V1 = C2V2, where C1=10 mM, C2=25 μM, V2=25 ml and V1 is the unknown:
  • Enter 10 into the Concentration (Start) box and choose the correct unit (mM)
  • Enter 25 into the Concentration (End) box and select the correct unit (mM)
  • Enter 25 into the Volume (End) box and choose the correct unit (mL)
  • Click the “Calculate” button
  • The answer of 62.5 μL (0.1 ml) appears in the Volume (Start) box
g/mol

Molecular Weight Calculator allows you to calculate the molar mass and elemental composition of a compound, as detailed below:

Note: Chemical formula is case sensitive: C12H18N3O4  c12h18n3o4
Instructions to calculate molar mass (molecular weight) of a chemical compound:
  • To calculate molar mass of a chemical compound, please enter the chemical/molecular formula and click the “Calculate’ button.
Definitions of molecular mass, molecular weight, molar mass and molar weight:
  • Molecular mass (or molecular weight) is the mass of one molecule of a substance and is expressed in the unified atomic mass units (u). (1 u is equal to 1/12 the mass of one atom of carbon-12)
  • Molar mass (molar weight) is the mass of one mole of a substance and is expressed in g/mol.
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Reconstitution Calculator allows you to calculate the volume of solvent required to reconstitute your vial.

  • Enter the mass of the reagent and the desired reconstitution concentration as well as the correct units
  • Click the “Calculate” button
  • The answer appears in the Volume (to add to vial) box
In vivo Formulation Calculator (Clear solution)
Step 1: Enter information below (Recommended: An additional animal to make allowance for loss during the experiment)
Step 2: Enter in vivo formulation (This is only a calculator, not the exact formulation for a specific product. Please contact us first if there is no in vivo formulation in the solubility section.)
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Calculation results

Working concentration mg/mL;

Method for preparing DMSO stock solution mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.

Method for preparing in vivo formulation:Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O,mix and clarify.

(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
             (2) Be sure to add the solvent(s) in order.

Biological Data
  • Structure of the DDB1ΔB-CRBN-dBET23-BRD4BD1 complex (a) The chemical structure of dBET23 is depicted with the target-moiety in red, the linker in black and cyan, and the E3-moiety in blue. (b) Cartoon representation of DDB1ΔB-CRBN-dBET23-BRD4BD1: DDB1 highlighting domains BPA (red), BPC (orange) and DDB1-CTD (grey); CRBN with domains NTD (blue), HBD (cyan) and CTD (green); BRD4BD1 (magenta). The Zn2+-ion is drawn as a grey sphere and dBET23 as sticks representation in yellow. The FO-FC map is shown as green mesh for dBET23 contoured at 3.0σ. (c) Superposition of DDB1ΔB-CRBN-dBET23-BRD4BD1 with CRBN bound to lenalidomide (pdb: 4tz4) and BRD4BD1 bound to JQ1-(S) (pdb: 3mxf). Surface representation for CRBN and BRD4BD1 are shown in gray and magenta, respectively. dBET23 is shown in yellow, JQ1 in green, and thalidomide in cyan. (d) Side-chain interactions between BRD4BD1, CRBN, and dBET23. Residues of BRD4BD1 mutated in this study are highlighted in cyan. Nat Chem Biol . 2018 Jul;14(7):706-714.
  • Plasticity of CRBN-substrate interactions (a) TR-FRET. dBET23 titrated to BRD4BD1-SPYCATCHER-BODIPY, Terbium-antiHis antibody and various His6-DDB1ΔB-CRBN wild type and His6-DDB1-CRBN mutant proteins. The mean peak heights for dose response curves of three independent replicates are shown as dot-plot. TR-FRET data in this figure is presented as means ± s.d. (b) surface representation of CRBN highlighting the residues involved in dBET23 mediated BRD4BD1 binding in orange (residues Y59, L60, Q86, Q100, F102, H103, P104, D149, F150, G151, I152, I154, K156, P352, H353, E377, H378). CRBN interface residues mutated for biochemical assays are indicated. (c) TR-FRET. dBET23 titrated to DDB1ΔB-CRBNSPYCATCHER-BODIPY, Terbium-Streptavidin and various BRD4BD1-biotin wild type and mutant proteins. The mean peak heights for dose response curves of three independent replicates are shown as dot-plot. TR-FRET data in this figure is presented as means ± s.d. (d) as in a but titrating dBET57. (e) surface representation of CRBN highlighting the BRD4BD1 interacting residues for the dBET57 mediated recruitment in orange (residues: Q325, H353, Y355, H357, I371, G372, R373, E377, V388, Q390, C394, A395, S396, H397, T418, S420). CRBN interface residues mutated for biochemical assays are indicated. (f) as in b but titrating dBET57. (g) Cartoon representation of DDB1ΔB-CRBN-dBET57-BRD4BD1: DDB1 highlighting domains BPA (red), BPC (orange) and DDB1-CTD (grey); CRBN with domains NTD (blue), HBD (cyan) and CTD (green); BRD4BD1 (magenta). The Zn2+-ion is drawn as a grey sphere. dBET57 was not modelled in this structure but instead superpositions of lenalidomide (from pdb: 5fqd) and JQ1 (from pdb: 3mxf) are shown in yellow sticks. (h) Superposition of CRBN and BRD4BD1 for the dBET23 and dBET57 containing complexes. Superposition was carried out over the CRBN-CTD (residues 320 – 400). (i) The chemical structures of dBET57 is depicted with the target-moiety in red, the linker in black and cyan, and the E3-moiety in blue. Nat Chem Biol . 2018 Jul;14(7):706-714.
  • Degrader mediated BRD4 recruitment is governed by negative cooperativity (a) TR-FRET. dBET23 titrated to DDB1ΔB-CRBNSPY-BODIPY, Terbium-Streptavidin and various BRD4BD1-biotin wild type and mutant proteins. The mean peak heights for dose response curves of three independent replicates are shown as dot-plot. Data in this figure is presented as means ± s.d. (n=3). (b) Competitive binding assay for dBET1 binding to DDB1ΔB-CRBN. Increasing concentrations of dBET1 titrated to preformed DDB1ΔB-CRBN-lenalidomideAtto565 complex in presence or absence of BRD4BD1 or BRD4BD2. (c) As in b but using dBET6, (d) dBET23, or (e) dBET57. All data in this figure are independent replicates presented as means ± s.d. (n=3). Nat Chem Biol . 2018 Jul;14(7):706-714.
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