PROTAC BRD9 Degrader-1 is a PROTAC protein degrader linked by Cereblon ligand and BRD9 ligand, which can be used as a selective probe to study BAF complexes.

Physicochemical Properties

Molecular Formula	C42H45N7O12S2
Molecular Weight	903.976407766342
Exact Mass	903.256
CAS #	2097971-01-0
PubChem CID	137628637
Appearance	Light yellow to yellow solid powder
LogP	0.8
Hydrogen Bond Donor Count	4
Hydrogen Bond Acceptor Count	14
Rotatable Bond Count	16
Heavy Atom Count	63
Complexity	1960
Defined Atom Stereocenter Count	0
SMILES	S1(CCC(CC1)/N=C(/C1=CC2C(N(C)C=C(C3C=CC(=C(C=3)OC)OCC(NCCCCNC(COC3=CC=CC4=C3C(N(C4=O)C3C(NC(CC3)=O)=O)=O)=O)=O)C=2S1)=O)\N)(=O)=O
InChi Key	LOLHUPGCPDURJG-UHFFFAOYSA-N
InChi Code	InChI=1S/C42H45N7O12S2/c1-48-20-27(37-26(40(48)54)19-32(62-37)38(43)46-24-12-16-63(57,58)17-13-24)23-8-10-29(31(18-23)59-2)60-21-34(51)44-14-3-4-15-45-35(52)22-61-30-7-5-6-25-36(30)42(56)49(41(25)55)28-9-11-33(50)47-39(28)53/h5-8,10,18-20,24,28H,3-4,9,11-17,21-22H2,1-2H3,(H2,43,46)(H,44,51)(H,45,52)(H,47,50,53)
Chemical Name	N-[4-[[2-[2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindol-4-yl]oxyacetyl]amino]butyl]-2-[4-[2-[N'-(1,1-dioxothian-4-yl)carbamimidoyl]-5-methyl-4-oxothieno[3,2-c]pyridin-7-yl]-2-methoxyphenoxy]acetamide
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: Please store this product in a sealed and protected environment (e.g. under nitrogen), avoid exposure to moisture.
Shipping Condition	Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)

Biological Activity

ln Vitro	BRD9, BRD4, and CRBN-DDB1 are all inhibited by PROTAC BRD9 Degrader-1 (Compound 1), with IC50 values of 13.5 nM, 3.78 μM, and 48.9 nM, respectively[1].
References	[1]. Degradation of the BAF Complex Factor BRD9 by Heterobifunctional Ligands. Angew Chem Int Ed Engl. 2017 May 15;56(21):5738-5743.

Solubility Data

Solubility (In Vitro)

DMSO : ~150 mg/mL (~165.93 mM)

Solubility (In Vivo)

Solubility in Formulation 1: ≥ 2.5 mg/mL (2.77 mM) (saturation unknown) in 10% DMSO + 40% PEG300 + 5% Tween80 + 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 25.0 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. Solubility in Formulation 2: ≥ 2.5 mg/mL (2.77 mM) (saturation unknown) in 10% DMSO + 90% (20% SBE-β-CD in 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 25.0 mg/mL clear DMSO stock solution to 900 μL of 20% SBE-β-CD physiological saline solution and mix evenly. Preparation of 20% SBE-β-CD in Saline (4°C，1 week): Dissolve 2 g SBE-β-CD in 10 mL saline 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	1.1062 mL	5.5311 mL	11.0622 mL
	5 mM	0.2212 mL	1.1062 mL	2.2124 mL
	10 mM	0.1106 mL	0.5531 mL	1.1062 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.