ITF-3985 HDAC6 is a novel HDAC6 inhibitor.

Physicochemical Properties

Molecular Formula	C13H9F2N7O2
Molecular Weight	333.2588
Exact Mass	333.0786
Elemental Analysis	C, 46.85; H, 2.72; F, 11.40; N, 29.42; O, 9.60
Appearance	Solid powder
LogP	0.7
Hydrogen Bond Donor Count	2
Hydrogen Bond Acceptor Count	9
Rotatable Bond Count	4
Heavy Atom Count	24
Complexity	429
Defined Atom Stereocenter Count	0
SMILES	3,5-difluoro-N-hydroxy-4-[(5-pyrimidin-2-yltetrazol-2-yl)methyl]benzamide
InChi Key	IAJVLFQKWJCAML-UHFFFAOYSA-N
InChi Code	InChI=1S/C13H9F2N7O2/c14-9-4-7(13(23)20-24)5-10(15)8(9)6-22-19-12(18-21-22)11-16-2-1-3-17-11/h1-5,24H,6H2,(H,20,23)
Chemical Name	3,5-difluoro-N-hydroxy-4-[(5-pyrimidin-2-yltetrazol-2-yl)methyl]benzamide
Synonyms	ITF3985; ITF-3985; CHEMBL4470373; 3,5-bis(fluoranyl)-~{N}-oxidanyl-4-[(5-pyrimidin-2-yl-1,2,3,4-tetrazol-2-yl)methyl]benzamide; SCHEMBL23316873; BDBM50531051; 3,5-Difluoro-N-hydroxy-4-((5-(pyrimidin-2-yl)-2H-tetrazol-2-yl)methyl)benzamide; V05; ITF 3985
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
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

Targets	HD1-B (IC50 = 7.5 nM); HD2 (IC50 = 10 nM); HD1-A (IC50 = 16 nM)
ln Vitro	Nonselective histone deacetylase (HDAC) inhibitors show dose-limiting side effects due to the inhibition of multiple, essential HDAC subtypes that can be limited or prevented by restricting their selectivity. We herein report the crystal structures of zebrafish HDAC6 catalytic domain 2 (zHDAC6-CD2) in complex with the selective HDAC6 inhibitors ITF3756 and ITF3985 and shed light on the role of fluorination in the selectivity of benzohydroxamate-based structures over class I isoforms. The reason for the enhancement in the selectivity of the benzohydroxamate-based compounds is the presence of specific interactions between the fluorinated linker and the key residues Gly582, Ser531, and His614 of zHDAC6, which are hindered in class I HDAC isoforms by the presence of an Aspartate that replaces Ser531. These results can be used in the design and development of novel, highly selective HDAC6 inhibitors.[1]
References	[1]. Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors. ACS Med Chem Lett . 2021 Oct 11;12(11):1810-1817.
Additional Infomation	ITF3985 (2-FF) in zCD2 (2.30 Å resolution) aligned with the unbound enzyme exhibits a slightly larger rmsd (0.52 Å) compared to that of ITF3756. Only one monomer is present in the asymmetric unit (Table S3), and the benzyl hydroxamate moiety shares several common features with ITF3756. The hydroxamate group reveals monodentate coordination to Zn2+ with the sp3 oxygen directly bound to the metal ion (Figure 3B and Figure S2), whereas a water molecule directly binds the Zn2+ and makes HBs with Asp612, His573, His574, and the carbonyl oxygen atom of the hydroxamate (O···O distance equal to 2.81 Å). The phenyl substructure is sandwiched between Phe583 and Phe643 with the usual π–π stacking interaction. The fluorine atom that faces the loop L2 residues apparently interacts (as determined by Discovery Studio Visualizer 2020, automatic noncovalent bond recognition) with the Cβ of Ser531 and the Cα of Gly582 via a C–H···F weak HB. It should be of note that HBs involving fluorine atoms are controversial from both the experimental and theoretical points of view.19,20 Despite the poor propensity of the fluorine atom to engage in noncovalent bonds (halogen bonds are rarely reported),21 there is evidence of a possible weak noncovalent interaction between the small electronegative halogen and the backbone’s carbonyl moiety.22 Indeed, several X-ray structures have reported F···C=O distances23 in the 3.0 Å −3.7 Å range, even if the details of such bonds are still unclear. [1]

Solubility Data

Solubility (In Vitro)

DMSO: ~95 mg/mL (~199.6 mM)

Solubility (In Vivo)

Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples. Injection Formulations (e.g. IP/IV/IM/SC) Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] *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. Injection Formulation 5: 2-Hydroxypropyl-β-cyclodextrin : Saline = 50 : 50 (i.e. 500 μL 2-Hydroxypropyl-β-cyclodextrin → 500 μL Saline) Injection Formulation 6: DMSO : PEG300 : castor oil : Saline = 5 : 10 : 20 : 65 (i.e. 50 μL DMSO → 100 μLPEG300 → 200 μL castor oil → 650 μL Saline) Injection Formulation 7: Ethanol : Cremophor : Saline = 10： 10 : 80 (i.e. 100 μL Ethanol → 100 μL Cremophor → 800 μL Saline) Injection Formulation 8: Dissolve in Cremophor/Ethanol (50 : 50), then diluted by Saline Injection Formulation 9: EtOH : Corn oil = 10 : 90 (i.e. 100 μL EtOH → 900 μL Corn oil) Injection Formulation 10: EtOH : PEG300：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL EtOH → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Oral Formulations Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). Oral Formulation 3: Dissolved in PEG400 Oral Formulation 4: Suspend in 0.2% Carboxymethyl cellulose Oral Formulation 5: Dissolve in 0.25% Tween 80 and 0.5% Carboxymethyl cellulose Oral Formulation 6: Mixing with food powders Note: Please be aware that the above formulations are for reference only. InvivoChem strongly recommends customers to read literature methods/protocols carefully before determining which formulation you should use for in vivo studies, as different compounds have different solubility properties and have to be formulated differently.  (Please use freshly prepared in vivo formulations for optimal results.)

Preparing Stock Solutions		1 mg	5 mg	10 mg
	1 mM	3.0007 mL	15.0033 mL	30.0066 mL
	5 mM	0.6001 mL	3.0007 mL	6.0013 mL
	10 mM	0.3001 mL	1.5003 mL	3.0007 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.