Tubastatin A

Protein target name:

HDAC6, HDAC10

Mechanism of action:

Inhibitor, Class IIB

Recommended Concentration for use in cells:

1 uM

Probe Availability

Abcam (1239262-52-2)

Cayman Chemicals

Probe Information

Target and Probe Information

Target Details

Target class:

Epigenetics

Subclass:

HDAC

HUGO ID:

HGNC:14064 HGNC:18128

Entrez gene ID:

10013 83933

UNIPROT ID:

Q9UBN7 Q969S8

Target alias:

CPBHM, HD6, JM21, PPP1R90, HD10

Probe Details

Chemical Probes Portal ID:

CPP1000

Probe alias:

Tubastatin-A

PubChem CID:

49850262

ChEMBL ID:

CHEMBL2018302

SMILES string:

CN1CCC2=C(C1)C3=CC=CC=C3N2CC4=CC=C(C=C4)C(=O)NO

InChi Key:

GOVYBPLHWIEHEJ-UHFFFAOYSA-N

Control compound:

Compound 27 (4-((2-(tert-Butyl)-1H-indol-1-yl)methyl)-N-hydroxybenzamide)

Orthogonal probe:

HPOBNexturastat ASS-208

Physico-chemical properties

Solubility - preferred solvent:

DMSO

NMR:

1H NMR (400 MHz, DMSO): δ 11.17 (br, 1H), 10.17 (br, 1H), 9.00 (br, 1H), 7.67 (d, 2H, J = 7.9 Hz), 7.48 (t, 2H, J = 7.9 Hz), 7.17-7.06 (m, 4H), 5.44 (br, 2H), 4.50 (br, 2H), 3.60 (br, 2H), 3.10 (m, 2H), 3.00 (s, 3H).

13C NMR APT (100 MHz, MeOD): δ 141.5 (up), 137.0 (up), 132.3 (up), 131.7 (up), 127.7 (down), 126.9 (down), 124.8 (up), 122.3 (down), 120.2 (down), 118.2 (down), 110.6 (down), 102.7 (up), 51.0 (up), 50.6 (up), 46.0 (up), 42.3 (down), 20.1 (up).

Storage Recommendations

Storage (dry powder):

-20

Validation in Cells and Model Organisms

In vitro validation

On target activity

Potency:

IC50

15 nM (HDAC6) 12.6 nM (HDAC10)

Potency assay:

Enzyme inhibition assays were performed by the Reaction Biology Corporation, Malvern, PA, using the Reaction Biology HDAC Spectrum platform and by TR-FRET following displacement of radio-labeled compound.

PDB ID for probe-target interaction (3D structure):

3FOR, 5EDU

Structure-activity relationship:

yes, see 10.1021/acs.jmedchem.8b01936 for reference.

Off target activity

Potency (off target):

IC50

Off target protein and potency:

HDAC8 854 nM

Potency assay (off target):

Enzyme inhibition assays using the Reaction Biology HDAC Spectrum platform.

In cell validation

On target activity in cells

Potency in cells:

pIC50

7.0 (HDAC6), 7.9 (HDAC10)

Potency assay (cells):

A bioluminescence resonance energy transfer (BRET) assay that measures displacement of a fluorescently-labeled ligand was used with cells that overexpress nano-luciferase-tagged HDAC10.

Target engagement assay (cells):

The BRET assay can provides target engagement values in living cells. (see ref. doi/10.1021/acs.jmedchem.8b01936)

In vivo validation

Organism:

Mouse (Pkd1fl/fl;Pax8rtTA;TetO-cre)

Dose:

5 mg/Kg IV30 mg/Kg Oral

Route of delivery:

OralIntravenous

Plasma half life:

0.35 h

Systemic clearance:

222 ml/min/Kg

Cmax:

135 ng/mL

Tmax:

0.25 h

Organ of Interest

Organ (O):

Kidney

Primary Reference

Reference (doi):

10.1021/ja102758v 10.1128/MCB.05155-11 10.1021/acs.jmedchem.8b01936 10.1074/jbc.M117.803775

Reference (PMID):

20614936 21444725 30964290 28887310

Under Review

This probe is in the process of SAB review. Please continue to check back for new reviews and commentary.

SAB Rating

Rating for use in Cells

2 review(s)

Rating for use in Model Organisms

2 review(s)

SAB Members

SAB Comments

This compound has been claimed to be HDAC6 selective except by DOI: 10.1021/acs.jmedchem.8b01936 where this compound was shown to be more active in HDAC10 by FRET and BRET (cellular) assays

Jun 2 2020 - 1:47pm

The biology of HDAC6 and HDAC10 are likely to be very different so, this probe should be used in combination with genetic knockdown and/or other more selective compounds for either HDAC6 or HDAC10 (see for example Geraldy et al J. Med. Chem. 2019, 62, 9, 4426–4443) in order to attribute affects of Tubistatin A to one of these enzymes.

Jun 28 2020 - 8:47am

Tubastatin A

Probe Availability

Probe Information

Target Details

CPBHM, HD6, JM21, PPP1R90, HD10

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

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Tubastatin A

Probe Availability

Probe Information

Target Details

CPBHM, HD6, JM21, PPP1R90, HD10

Probe Details

Physico-chemical properties

In vitro validation

In cell validation

In vivo validation

Primary Reference

Supporting Organizations

Interested in supporting the portal?