Cat. No.: HY-13322

Pracinostat

(Synonyms: SB939)

9 Cited Publications

Customer Review

Based on 9 publication(s) in Google Scholar

Pracinostat is a potent histone deacetylase (HDAC) inhibitor, with IC₅₀s of 40-140 nM, used for cancer research. Pracinostat also inhibits metallo-β-lactamase domain-containing protein 2 (MBLAC2) hydrolase activity with an EC₅₀ below 10 nM.

For research use only. We do not sell to patients.

Purity: 99.80%
CAS No.: 929016-96-6
Formula: C₂₀H₃₀N₄O₂
Molecular Weight:358.48

Storage:

Powder -20°C, 3 years ; In solvent -80°C, 6 months , -20°C, 1 month

Pracinostat Chemical Structure

CAS No.: 929016-96-6

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Top Publications Citing

Use of MCE Products

Fluorescent Dye

Strong Fluorescence Signal / Multi-Disciplinary Applications / High Fluorescence Specificity

Biological Activity
- Description
- IC₅₀ & Target
- Cellular Effect
- In Vitro
- In Vivo
- Clinical Trial
Chemical Information
Publications (9)
Solvent & Solubility
- In Vitro
- In Vivo
Protocol
Purity & Documentation
References
Help & FAQs
Classifications
Bioz

Biological Activity

Description

IC₅₀ & Target^[1]^[4]

HDAC10

40 nM (IC₅₀)

HDAC3

43 nM (IC₅₀)

HDAC5

47 nM (IC₅₀)

HDAC1

49 nM (IC₅₀)

HDAC4

56 nM (IC₅₀)

HDAC9

70 nM (IC₅₀)

HDAC11

93 nM (IC₅₀)

HDAC2

96 nM (IC₅₀)

HDAC7

137 nM (IC₅₀)

HDAC8

140 nM (IC₅₀)

HDAC6

1008 nM (IC₅₀)

MBLAC2

<10 nM (EC₅₀)

All Beta-lactamase Isoforms :

All HDAC Isoforms :

Cellular Effect

Cell Line	Type	Value	Description	References
HCT-116	GI₅₀	0.24 μM Compound: 3, SB939	Antiproliferative activity against human HCT116 cells after 48 hrs by sulforhodamine B assay Antiproliferative activity against human HCT116 cells after 48 hrs by sulforhodamine B assay	[PMID: 24119555]
HeLa	IC₅₀	126 nM Compound: 3, SB939	Inhibition of HDAC in human HeLa cell nuclear extracts using Fluor de Lys as substrate by fluorescence assay Inhibition of HDAC in human HeLa cell nuclear extracts using Fluor de Lys as substrate by fluorescence assay	[PMID: 24119555]
HepG2	IC₅₀	0.15 μM Compound: SB939	Antimalarial activity against exo-erythrocytic form of Plasmodium berghei infected in human HepG2 cells Antimalarial activity against exo-erythrocytic form of Plasmodium berghei infected in human HepG2 cells	[PMID: 24904967]
MCF7	GI₅₀	0.17 μM Compound: 3, SB939	Antiproliferative activity against human MCF7 cells after 48 hrs by sulforhodamine B assay Antiproliferative activity against human MCF7 cells after 48 hrs by sulforhodamine B assay	[PMID: 24119555]
MCF7	IC₅₀	5.34 μM Compound: 21; SB939	Cytotoxicity against human MCF7 cells assessed as inhibition of cell growth by MTS assay Cytotoxicity against human MCF7 cells assessed as inhibition of cell growth by MTS assay	[PMID: 32791404]
MDA-MB-231	IC₅₀	5.34 μM Compound: 21; SB939	Cytotoxicity against human MDA-MB-231 cells assessed as inhibition of cell growth by MTS assay Cytotoxicity against human MDA-MB-231 cells assessed as inhibition of cell growth by MTS assay	[PMID: 32791404]
MDA-MB-435	GI₅₀	0.48 μM Compound: 3, SB939	Antiproliferative activity against human MDA-MB-435 cells after 48 hrs by sulforhodamine B assay Antiproliferative activity against human MDA-MB-435 cells after 48 hrs by sulforhodamine B assay	[PMID: 24119555]
NCI-H460	GI₅₀	0.22 μM Compound: 3, SB939	Antiproliferative activity against human NCI-H460 cells after 48 hrs by sulforhodamine B assay Antiproliferative activity against human NCI-H460 cells after 48 hrs by sulforhodamine B assay	[PMID: 24119555]
OVCAR-5	GI₅₀	0.61 μM Compound: 3, SB939	Antiproliferative activity against human OVCAR5 cells after 48 hrs by sulforhodamine B assay Antiproliferative activity against human OVCAR5 cells after 48 hrs by sulforhodamine B assay	[PMID: 24119555]
T47D	IC₅₀	5.34 μM Compound: 21; SB939	Cytotoxicity against human T47D cells assessed as inhibition of cell growth by MTS assay Cytotoxicity against human T47D cells assessed as inhibition of cell growth by MTS assay	[PMID: 32791404]

In Vitro

Pracinostat (SB939) is a potent novel hydroxamate-based inhibitor of HDACs class I, II, and IV, inhibiting the isolated enzymes with a K_i of 19 to 48 nM (class I), 16 to 247 nM (class II), and 43 nM (class IV), but with no activity against the class III isoenzyme SIRT I. SB939 has effects on HCT-116 colon cancer cell line and the HL-60 acute myeloid leukemia cell line, with IC₅₀s of 0.48 μM and 70 nM, respectively. SB939 does not inhibit the proliferation of normal human dermal fibroblasts at concentrations up to 100 μM^[1]. Pracinostat (SB939, compound 3) inhibits CYP2C19 with IC₅₀ of 5.78 μM. SB939 shows potent activities against A2780, COLO 205, HCT-116, and PC-3 cell lines, with IC₅₀s of 0.48 ± 0.21, 0.56 ± 0.08, 0.48 ± 0.27, and 0.34 ± 0.06^[2]. Pracinostat downregulates JAK and FLT3 signaling in JAK2^V617F and FLT-ITD cell lines, and shows synergy in combination with pacritinib. Pracinostat and pacritinib show in vitro synergy on STAT signaling and apoptosis. Pracinostat potently inhibits proliferation of different AML subtypes as a single agent and is synergistic with pacritinib in JAK2^V617F or FLT3-ITD AML cell lines^[3].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

In Vivo

Pracinostat (SB939, 25-100 mg/kg) shows significant dose-dependent growth inhibition of HCT-116 xenografts. SB939 selectively accumulates in tumor tissue. SB939 (50 or 75 mg/kg) exhibits anti-tumor activities in the Apcmin genetic colon cancer mouse model^[1]. Pracinostat (25 or 50 mg/kg per day for 21 days) induces significant inhibition of tumor growth (TGI), by 59 and 116%, respectively, in mice bearing MV4-11 xenografts. Pracinostat (75 mg/kg, q.o.d) in combination with pacritinib is efficacious and synergistic in vivo in two different models of human AML. Pracinostat and pacritinib have synergistic effects on AML-induced plasma cytokines/growth factors/chemokines^[3].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

Clinical Trial

NCT Number	Sponsor	Condition	Start Date	Phase A549
NCT01329991	Plexxikon\|		2011-05	PHASE1

Chemical Information

CAS No. 929016-96-6
Appearance Solid
Molecular Weight 358.48
Formula C₂₀H₃₀N₄O₂
Color White to light brown
SMILES

ONC(/C=C/C1=CC=C2N(C(CCCC)=NC2=C1)CCN(CC)CC)=O
Synonyms

SB939
Shipping

Room temperature in continental US; may vary elsewhere.

Storage

Powder	-20°C	3 years
In solvent	-80°C	6 months
	-20°C	1 month

Publications (9)

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Proc Natl Acad Sci U S A

MGMT-activated DUB3 stabilizes MCL1 and drives chemoresistance in ovarian cancer. [Abstract]

2019 Feb 19;116(8):2961-2966. PMID: 30718431
Drug Des Devel Ther

Advances in the drug therapies of acute myeloid leukemia (except acute wpromyelocytic leukemia). [Abstract]

2018 Apr 30:12:1009-1017. PMID: 29750014
J Mol Med (Berl)

Combination of PARP inhibitor and temozolomide to suppress chordoma progression. [Abstract]

2019 Aug;97(8):1183-1193. PMID: 31201471
Int J Parasitol Drugs Drug Resist

2026 May 17;31:100649.
bioRxiv

2025 Aug 25.
bioRxiv

2025 January 15.
bioRxiv

2024 Jan 16.
SSRN

2023 Jun 20.
bioRxiv

2021 Jan 5.

Solvent & Solubility

In Vitro:

DMSO : 250 mg/mL (697.39 mM; Need ultrasonic; Hygroscopic DMSO has a significant impact on the solubility of product, please use newly opened DMSO)

View the Complete Stock Solution Preparation Table

Preparing Stock Solutions

View the Complete Stock Solution Preparation Table

Concentration Solvent Mass

1 mg

5 mg

10 mg

Concentration

Solvent

Mass

1 mM

2.7896 mL

13.9478 mL

27.8956 mL

5 mM

0.5579 mL

2.7896 mL

5.5791 mL

10 mM

0.2790 mL

1.3948 mL

2.7896 mL

Please refer to the solubility information to select the appropriate solvent. Once prepared, please aliquot and store the solution to prevent product inactivation from repeated freeze-thaw cycles.

Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

Molarity Calculator

Mass (g) = Concentration (mol/L) × Volume (L) × Molecular Weight (g/mol)

Mass Mass

Concentration Concentration

Volume Volume

Molecular Weight Molecular Weight

Dilution Calculator

Concentration _(start) × Volume _(start) = Concentration _(final) × Volume _(final)

Concentration _(start) Concentration _(start)

Volume _(start) Volume _(start)

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In Vivo:

Select the appropriate dissolution method based on your experimental animal and administration route.

Stock Solution Working Solution

For the following dissolution methods, please ensure to first prepare a clear stock solution using an In Vitro approach and then sequentially add co-solvents:
To ensure reliable experimental results, the clarified stock solution can be appropriately stored based on storage conditions. As for the working solution for In Vivo experiments, it is recommended to prepare freshly and use it on the same day.
The percentages shown for the solvents indicate their volumetric ratio in the final prepared solution. If precipitation or phase separation occurs during preparation, heat and/or sonication can be used to aid dissolution.

Protocol 1

Add each solvent one by one: 10% DMSO 90% (20% SBE-β-CD in Saline)

Solubility: ≥ 2.75 mg/mL (7.67 mM); Clear solution

This protocol yields a clear solution of ≥ 2.75 mg/mL (saturation unknown).

Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (27.5 mg/mL) to 900 μL 20% SBE-β-CD in Saline, and mix evenly.

Protocol 2

Add each solvent one by one: 10% DMSO 40% PEG300 5% Tween-80 45% Saline

Solubility: ≥ 2.08 mg/mL (5.80 mM); Clear solution

This protocol yields a clear solution of ≥ 2.08 mg/mL (saturation unknown).

Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (20.8 mg/mL) to 400 μL PEG300, and mix evenly; then add 50 μL Tween-80 and mix evenly; then add 450 μL Saline to adjust the volume to 1 mL.

Protocol 3

Add each solvent one by one: 10% DMSO 90% Corn Oil

Solubility: ≥ 2.08 mg/mL (5.80 mM); Clear solution

This protocol yields a clear solution of ≥ 2.08 mg/mL (saturation unknown). If the continuous dosing period exceeds half a month, please choose this protocol carefully.

Taking 1 mL working solution as an example, add 100 μL DMSO stock solution (20.8 mg/mL) to 900 μL Corn oil, and mix evenly.

In Vivo Dissolution Calculator

Please enter the basic information of animal experiments:

Dosage Dosage
mg/kg
Animal Weight (Per Animal) Animal Weight (Per Animal)
g
Dosing Volume (Per Animal) Dosing Volume (Per Animal)
μL
Number of Animals Number of Animals

Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.

Recommended: Prepare an additional quantity of animals to account for potential losses during experiments.

Please enter your animal formula composition:

%
DMSO +

Recommended: Keep the proportion of DMSO in working solution below 2% if your animal is weak.
%
+
+
%
Tween-80 + +
%
Saline +

The co-solvents required include: DMSO, . All of co-solvents are available by MedChemExpress (MCE). , Tween 80. All of co-solvents are available by MedChemExpress (MCE).

Working solution concentration: 0.22 mg/mL

Protocol

Cell Assay^[1]

Cells are seeded in 96-well plates at a predetermined optimal density, in the log growth phase, and rested for 24 h (adherent cells) or 2 h (suspension cells), respectively, before treatment with SB939. All experiments are done in triplicates for 96 h, with 1% solvent, using either the CyQUANT Cell proliferation assay kit for adherent cells or the CellTiter96 Aqueous One solution cell proliferation kit for suspension cells, in a total volume of 100 μL with SB939 concentrations from 100 μM to 1.5 nM in nine serial dilution steps. IC₅₀ are determined using the XLfit software^[1].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

Animal Administration^[1]

Male Apc^Min/+ mice and female C57BL/6 mice are fed a standard rodent diet. Mice with the confirmed mutation, between 16 and 20.5 wk of age, with a positive scoring in the hemocult assay are recruited to the experiment. During treatment, mice are injected i.p. with 40 mg/kg of 5-FU in a volume of 200 μL per 20 g body weight, once daily, for 5 d of treatment, followed by a 9-d recovery period and an additional 5 d of treatment. Treatment with SB939 per oral at 50 or 75 mg/kg once daily is given continuously for 21 d. At the last day of the treatment, the small intestine, caecum, and colon are removed; fixed by multiple injections of 4% PBS-buffered formaldehyde into the gut lumen; cut into segments; and spread flat on a plastic film in a formaldehyde bath. Tumor load is measured in a dissection microscope. Assessment and analysis of the samples are done blinded^[1].

MedChemExpress (MCE) has not independently confirmed the accuracy of these methods. They are for reference only.

Purity & Documentation

Select Batch:

Purity: 99.98%

Assay: 99.98%

ee.: 99.98%

Data Sheet (280 KB)
SDS (604 KB)
- English - EN (604 KB)
- Français - FR (604 KB)
- Deutsch - DE (604 KB)
- Norwegian - NO (604 KB)
- Español - ES (604 KB)
- Swedish - SV (604 KB)
- Italian - IT (604 KB)
- Korean - KR (604 KB)
- Portuguese - PT (604 KB)
COA (2659 KB)
Elemental Analysis Report (2659 KB)
HNMR (2659 KB)
CNMR (2659 KB)
RP-HPLC (2659 KB)
NP-HPLC (2659 KB)
MS (2659 KB)
LCMS (2659 KB)
IR (2659 KB)
GC (2659 KB)
OR (2659 KB)
SDS-PAGE (2659 KB)
SEC-HPLC (2659 KB)
Other Report (2659 KB)
Handling Instructions (2659 KB)

References

[1]. Novotny-Diermayr V, et al. SB939, a novel potent and orally active histone deacetylase inhibitor with high tumor exposure and efficacy in mouse models of colorectal cancer. Mol Cancer Ther. 2010 Mar;9(3):642-52. [Content Brief]

[2]. Wang H, et al. Discovery of (2E)-3-{2-butyl-1-[2-(diethylamino)ethyl]-1H-benzimidazol-5-yl}-N-hydroxyacrylamide (SB939), an orally active histone deacetylase inhibitor with a superior preclinical profile. J Med Chem. 2011 Jul 14;54(13):4694-720. [Content Brief]

[3]. Novotny-Diermayr V, et al. The oral HDAC inhibitor pracinostat (SB939) is efficacious and synergistic with the JAK2 inhibitor pacritinib (SB1518) in preclinical models of AML. Blood Cancer J. 2012 May;2(5):e69. [Content Brief]

[4]. Lechner S, et al. Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target. Nat Chem Biol. 2022 Aug;18(8):812-820. [Content Brief]

Help & FAQs

How should lyophilized recombinant proteins be reconstituted and stored?

1. Before opening the cap, centrifuge the vial at 13000 rpm for 20-30 seconds. This step will ensure that any lyophilized powder that may have adhered to the cap or walls is collected at the bottom of the vial, minimizing the risk of product loss.

Complete Stock Solution Preparation Table

Storage method and period of stock solution: -80°C, 6 months; -20°C, 1 month. When stored at -80°C, please use it within 6 months. When stored at -20°C, please use it within 1 month.

Optional Solvent	Concentration Solvent Mass	1 mg	5 mg	10 mg	25 mg
DMSO	1 mM	2.7896 mL	13.9478 mL	27.8956 mL	69.7389 mL
	5 mM	0.5579 mL	2.7896 mL	5.5791 mL	13.9478 mL
	10 mM	0.2790 mL	1.3948 mL	2.7896 mL	6.9739 mL
	15 mM	0.1860 mL	0.9299 mL	1.8597 mL	4.6493 mL
	20 mM	0.1395 mL	0.6974 mL	1.3948 mL	3.4869 mL
	25 mM	0.1116 mL	0.5579 mL	1.1158 mL	2.7896 mL
	30 mM	0.0930 mL	0.4649 mL	0.9299 mL	2.3246 mL
	40 mM	0.0697 mL	0.3487 mL	0.6974 mL	1.7435 mL
	50 mM	0.0558 mL	0.2790 mL	0.5579 mL	1.3948 mL
	60 mM	0.0465 mL	0.2325 mL	0.4649 mL	1.1623 mL
	80 mM	0.0349 mL	0.1743 mL	0.3487 mL	0.8717 mL
	100 mM	0.0279 mL	0.1395 mL	0.2790 mL	0.6974 mL

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Pracinostat

Anti-Infection Compound Library

Apoptosis Compound Library

Cell Cycle/DNA Damage Compound Library

Epigenetics Compound Library

FDA-Approved Drug Library

Histone Modification Research Compound Library

Anti-Cancer Compound Library

Anti-Aging Compound Library

Drug Repurposing Compound Library

Covalent Screening Library

Reprogramming Compound Library

Oxygen Sensing Compound Library

FDA Approved & Pharmacopeial Drug Library

Anti-Breast Cancer Compound Library

Anti-Pancreatic Cancer Compound Library

Anti-Blood Cancer Compound Library

Anti-Liver Cancer Compound Library

Rare Diseases Drug Library

EMA-Approved Drug Library

FDA-Approved Anticancer Drug Library

Human Metabolite Library

Anti-Prostate Cancer Compound Library

Anti-Pulmonary Fibrosis Compound Library

Osteogenesis Compound Library

Off-patent Drug Library

Cell Death Library

Anti-Hematopathy Compound Library

Multi-Target Compound Library

Bioactive Compound Library Max

MCE Bioactive Compound Library

Covalent Screening Library Plus

Drug Repurposing Compound Library Plus

FDA-Approved Drug Library Plus

FDA-Approved Drug Library Mini

Bioactive Compound Library

Anti-Brain Cancer Compound Library

Non-Alcoholic Fatty Liver Disease (NAFLD) Compound Library

High-Throughput Bioactive Compound Library

Mass Spectrometry Human Metabolite Library

High-Efficiency Gene Editing Compound Library

Lactylation Compound Library

Publications Citing Use of MedChemExpress (MCE) Pracinostat

All Beta-lactamase Isoforms

All HDAC Isoforms

Biological Activity

Chemical Information

Publications (9)

Solvent & Solubility

Protocol

Purity & Documentation

References

Help & FAQs

Complete Stock Solution Preparation Table

Pracinostat Related Classifications

HY-13322 Related Classifications