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histone deacetylase 1

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Target id: 2658

Nomenclature: histone deacetylase 1

Family: 3.5.1.- Histone deacetylases (HDACs)

Contents:

Gene and Protein Information Click here for help
Species TM AA Chromosomal Location Gene Symbol Gene Name Reference
Human - 482 1p35.2-p35.1 HDAC1 histone deacetylase 1
Mouse - 482 4 63.26 cM Hdac1 histone deacetylase 1
Rat - 482 5q36 Hdac1 histone deacetylase 1
Database Links Click here for help
Alphafold Q13547 (Hs), O09106 (Mm)
BRENDA 3.5.1.98
CATH/Gene3D 3.40.800.20
ChEMBL Target CHEMBL325 (Hs), CHEMBL4001 (Mm)
DrugBank Target Q13547 (Hs)
Ensembl Gene ENSG00000116478 (Hs), ENSMUSG00000028800 (Mm), ENSRNOG00000009568 (Rn)
Entrez Gene 3065 (Hs), 433759 (Mm), 297893 (Rn)
Human Protein Atlas ENSG00000116478 (Hs)
KEGG Enzyme 3.5.1.98
KEGG Gene hsa:3065 (Hs), mmu:433759 (Mm), rno:297893 (Rn)
OMIM 601241 (Hs)
Pharos Q13547 (Hs)
RefSeq Nucleotide NM_004964 (Hs), NM_008228 (Mm), NM_001025409 (Rn)
RefSeq Protein NP_004955 (Hs), NP_032254 (Mm), NP_001020580 (Rn)
UniProtKB Q13547 (Hs), O09106 (Mm)
Wikipedia HDAC1 (Hs)
Enzyme Reaction Click here for help
EC Number: 3.5.1.98

Download all structure-activity data for this target as a CSV file go icon to follow link

Inhibitors
Key to terms and symbols View all chemical structures Click column headers to sort
Ligand Sp. Action Value Parameter Reference
romidepsin Small molecule or natural product Approved drug Primary target of this compound Click here for species-specific activity table Hs Inhibition 11.8 pKi 3
⤷ pKi 11.8 (Ki 1.5x10-12 M) [3]
apicidin Small molecule or natural product Click here for species-specific activity table Guide to Malaria Pharmacology Ligand Hs Inhibition 10.4 pKi 3
⤷ pKi 10.4 (Ki 4x10-11 M) [3]
trichostatin A Small molecule or natural product Primary target of this compound Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 9.7 pKi 3
⤷ pKi 9.7 (Ki 2x10-10 M) [3]
dacinostat Small molecule or natural product Click here for species-specific activity table Hs Inhibition 9.3 pKi 3
⤷ pKi 9.3 (Ki 5.5x10-10 M) [3]
belinostat Small molecule or natural product Approved drug Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 9.1 pKi 3
⤷ pKi 9.1 (Ki 8.5x10-10 M) [3]
vorinostat Small molecule or natural product Approved drug Primary target of this compound Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 8.9 pKi 3
⤷ pKi 8.9 (Ki 1.3x10-9 M) [3]
scriptaid Small molecule or natural product Click here for species-specific activity table Hs Inhibition 8.8 pKi 3
⤷ pKi 8.8 (Ki 1.5x10-9 M) [3]
givinostat Small molecule or natural product Approved drug Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 8.7 pKi 3
⤷ pKi 8.7 (Ki 2x10-9 M) [3]
mocetinostat Small molecule or natural product Click here for species-specific activity table Hs Inhibition 8.1 pKi 3
⤷ pKi 8.1 (Ki 9x10-9 M) [3]
entinostat Small molecule or natural product Click here for species-specific activity table Hs Inhibition 7.7 pKi 3
⤷ pKi 7.7 (Ki 2.2x10-8 M) [3]
RGFP109 Small molecule or natural product Click here for species-specific activity table Hs Inhibition 7.5 pKi 21
⤷ pKi 7.5 (Ki 3.2x10-8 M) [21]
tacedinaline Small molecule or natural product Primary target of this compound Click here for species-specific activity table Hs Inhibition 7.3 pKi 3
⤷ pKi 7.3 (Ki 5x10-8 M) [3]
panobinostat Small molecule or natural product Approved drug Click here for species-specific activity table Ligand has a PDB structure Guide to Malaria Pharmacology Ligand Hs Inhibition 8.5 pEC50 10
⤷ pEC50 8.5 (EC50 3x10-9 M) [10]
givinostat Small molecule or natural product Approved drug Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 7.6 pEC50 10
⤷ pEC50 7.6 (EC50 2.8x10-8 M) [10]
belinostat Small molecule or natural product Approved drug Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 7.4 pEC50 10
⤷ pEC50 7.4 (EC50 4.1x10-8 M) [10]
entinostat Small molecule or natural product Click here for species-specific activity table Hs Inhibition 6.7 pEC50 10
⤷ pEC50 6.7 (EC50 1.81x10-7 M) [10]
quisinostat Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Guide to Malaria Pharmacology Ligand Hs Inhibition 10.0 pIC50 1
⤷ pIC50 10.0 (IC50 1.1x10-10 M) [1]
compound 25ap [PMID: 37796543] Small molecule or natural product Click here for species-specific activity table Hs Inhibition 9.9 pIC50 26
⤷ pIC50 9.9 (IC50 1.2x10-10 M) [26]
martinostat Small molecule or natural product Click here for species-specific activity table Hs Inhibition 9.5 pIC50 24
⤷ pIC50 9.5 (IC50 3x10-10 M) [24]
fimepinostat Small molecule or natural product Click here for species-specific activity table Immunopharmacology Ligand Hs Inhibition 8.8 pIC50 20
⤷ pIC50 8.8 (IC50 1.7x10-9 M) [20]
CHR-3996 Small molecule or natural product Primary target of this compound Click here for species-specific activity table Hs Inhibition 8.5 pIC50 16
⤷ pIC50 8.5 (IC50 3x10-9 M) [16]
CUDC-101 Small molecule or natural product Click here for species-specific activity table Hs Inhibition 8.4 pIC50 5
⤷ pIC50 8.4 (IC50 4.5x10-9 M) [5]
abexinostat Small molecule or natural product Primary target of this compound Click here for species-specific activity table Hs Inhibition 8.1 pIC50 4
⤷ pIC50 8.1 (IC50 7x10-9 M) [4]
citarinostat Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 7.5 pIC50 8
⤷ pIC50 7.5 (IC50 3.5x10-8 M) [8]
resminostat Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 7.4 pIC50 14
⤷ pIC50 7.4 (IC50 4.25x10-8 M) [14]
pracinostat Small molecule or natural product Click here for species-specific activity table Hs Inhibition 7.3 pIC50 18
⤷ pIC50 7.3 (IC50 4.9x10-8 M) [18]
ricolinostat Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 7.2 pIC50 22
⤷ pIC50 7.2 (IC50 5.8x10-8 M) [22]
ACY-738 Small molecule or natural product Click here for species-specific activity table Hs Inhibition 7.0 pIC50 9
⤷ pIC50 7.0 (IC50 9.4x10-8 M) [9]
BML-281 Small molecule or natural product Click here for species-specific activity table Immunopharmacology Ligand Hs Inhibition 7.0 pIC50 12
⤷ pIC50 7.0 (IC50 1x10-7 M) [12]
suprastat Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 6.9 pIC50 17
⤷ pIC50 6.9 (IC50 1.17x10-7 M) [17]
J27644 Small molecule or natural product Click here for species-specific activity table Hs Inhibition 6.6 pIC50 25
⤷ pIC50 6.6 (IC50 2.31x10-7 M) [25]
KA1010 Small molecule or natural product Click here for species-specific activity table Immunopharmacology Ligand Hs Inhibition 6.4 pIC50 6
⤷ pIC50 6.4 (IC50 3.56x10-7 M) [6]
tacedinaline Small molecule or natural product Click here for species-specific activity table Hs Inhibition 6.2 pIC50 15
⤷ pIC50 6.2 (IC50 5.7x10-7 M) [15]
SS-208 Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Immunopharmacology Ligand Hs Inhibition 5.9 pIC50 23
⤷ pIC50 5.9 (IC50 1.39x10-6 M) [23]
nexturastat A Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Hs Inhibition 5.5 pIC50 2
⤷ pIC50 5.5 (IC50 3.002x10-6 M) [2]
tubastatin A Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Immunopharmacology Ligand Hs Inhibition 4.9 pIC50 11
⤷ pIC50 4.9 (IC50 1.38x10-5 M) [11]
butyric acid Small molecule or natural product Click here for species-specific activity table Ligand has a PDB structure Immunopharmacology Ligand Hs Inhibition 4.8 pIC50 7
⤷ pIC50 4.8 (IC50 1.6x10-5 M) [7]
valproic acid Small molecule or natural product Approved drug Ligand has a PDB structure Hs Inhibition 3.4 pIC50 19
⤷ pIC50 3.4 (IC50 4x10-4 M) [19]
tucidinostat Small molecule or natural product Approved drug Primary target of this compound Hs Inhibition - - 13
⤷ [13]
Immuno Process Associations
Immuno Process:  Immune regulation
Immuno Process:  Immune system development
Immuno Process:  Chemotaxis & migration
Immuno Process:  Cytokine production & signalling
General Comments
HDAC1 is a Class I histone deacetylase.

References

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1. Arts J, King P, Mariën A, Floren W, Beliën A, Janssen L, Pilatte I, Roux B, Decrane L, Gilissen R et al.. (2009) JNJ-26481585, a novel "second-generation" oral histone deacetylase inhibitor, shows broad-spectrum preclinical antitumoral activity. Clin Cancer Res, 15 (22): 6841-51. [PMID:19861438]

2. Bergman JA, Woan K, Perez-Villarroel P, Villagra A, Sotomayor EM, Kozikowski AP. (2012) Selective histone deacetylase 6 inhibitors bearing substituted urea linkers inhibit melanoma cell growth. J Med Chem, 55 (22): 9891-9. [PMID:23009203]

3. Bradner JE, West N, Grachan ML, Greenberg EF, Haggarty SJ, Warnow T, Mazitschek R. (2010) Chemical phylogenetics of histone deacetylases. Nat Chem Biol, 6 (3): 238-243. [PMID:20139990]

4. Buggy JJ, Cao ZA, Bass KE, Verner E, Balasubramanian S, Liu L, Schultz BE, Young PR, Dalrymple SA. (2006) CRA-024781: a novel synthetic inhibitor of histone deacetylase enzymes with antitumor activity in vitro and in vivo. Mol Cancer Ther, 5 (5): 1309-17. [PMID:16731764]

5. Cai X, Zhai HX, Wang J, Forrester J, Qu H, Yin L, Lai CJ, Bao R, Qian C. (2010) Discovery of 7-(4-(3-ethynylphenylamino)-7-methoxyquinazolin-6-yloxy)-N-hydroxyheptanamide (CUDc-101) as a potent multi-acting HDAC, EGFR, and HER2 inhibitor for the treatment of cancer. J Med Chem, 53 (5): 2000-9. [PMID:20143778]

6. Ellis JD, Neil DA, Inston NG, Jenkinson E, Drayson MT, Hampson P, Shuttleworth SJ, Ready AR, Cobbold M. (2016) Inhibition of Histone Deacetylase 6 Reveals a Potent Immunosuppressant Effect in Models of Transplantation. Transplantation, 100 (8): 1667-74. [PMID:27222932]

7. Fass DM, Shah R, Ghosh B, Hennig K, Norton S, Zhao WN, Reis SA, Klein PS, Mazitschek R, Maglathlin RL et al.. (2010) Effect of Inhibiting Histone Deacetylase with Short-Chain Carboxylic Acids and Their Hydroxamic Acid Analogs on Vertebrate Development and Neuronal Chromatin. ACS Med Chem Lett, 2 (1): 39-42. [PMID:21874153]

8. Huang P, Almeciga-Pinto I, Jarpe M, van Duzer JH, Mazitschek R, Yang M, Jones SS, Quayle SN. (2017) Selective HDAC inhibition by ACY-241 enhances the activity of paclitaxel in solid tumor models. Oncotarget, 8 (2): 2694-2707. [PMID:27926524]

9. Jochems J, Boulden J, Lee BG, Blendy JA, Jarpe M, Mazitschek R, Van Duzer JH, Jones S, Berton O. (2014) Antidepressant-like properties of novel HDAC6-selective inhibitors with improved brain bioavailability. Neuropsychopharmacology, 39 (2): 389-400. [PMID:23954848]

10. Khan N, Jeffers M, Kumar S, Hackett C, Boldog F, Khramtsov N, Qian X, Mills E, Berghs SC, Carey N et al.. (2008) Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors. Biochem J, 409 (2): 581-9. [PMID:17868033]

11. Kozikowski A, Butler KV, Kalin JH. (2014) HDAC inhibitors and therapeutic methods of using same. Patent number: US8748451. Assignee: The Board Of Trustees Of The University Of Illinois. Priority date: 22/07/2009. Publication date: 10/06/2014.

12. Kozikowski AP, Tapadar S, Luchini DN, Kim KH, Billadeau DD. (2008) Use of the nitrile oxide cycloaddition (NOC) reaction for molecular probe generation: a new class of enzyme selective histone deacetylase inhibitors (HDACIs) showing picomolar activity at HDAC6. J Med Chem, 51 (15): 4370-3. [PMID:18642892]

13. Liu L, Chen B, Qin S, Li S, He X, Qiu S, Zhao W, Zhao H. (2010) A novel histone deacetylase inhibitor Chidamide induces apoptosis of human colon cancer cells. Biochem Biophys Res Commun, 392 (2): 190-5. [PMID:20060381]

14. Mandl-Weber S, Meinel FG, Jankowsky R, Oduncu F, Schmidmaier R, Baumann P. (2010) The novel inhibitor of histone deacetylase resminostat (RAS2410) inhibits proliferation and induces apoptosis in multiple myeloma (MM) cells. Br J Haematol, 149 (4): 518-28. [PMID:20201941]

15. Methot JL, Chakravarty PK, Chenard M, Close J, Cruz JC, Dahlberg WK, Fleming J, Hamblett CL, Hamill JE, Harrington P et al.. (2008) Exploration of the internal cavity of histone deacetylase (HDAC) with selective HDAC1/HDAC2 inhibitors (SHI-1:2). Bioorg Med Chem Lett, 18 (3): 973-8. [PMID:18182289]

16. Moffat D, Patel S, Day F, Belfield A, Donald A, Rowlands M, Wibawa J, Brotherton D, Stimson L, Clark V et al.. (2010) Discovery of 2-(6-{[(6-fluoroquinolin-2-yl)methyl]amino}bicyclo[3.1.0]hex-3-yl)-N-hydroxypyrimidine-5-carboxamide (CHR-3996), a class I selective orally active histone deacetylase inhibitor. J Med Chem, 53 (24): 8663-78. [PMID:21080647]

17. Noonepalle S, Shen S, Ptáček J, Tavares MT, Zhang G, Stránský J, Pavlíček J, Ferreira GM, Hadley M, Pelaez G et al.. (2020) Rational Design of Suprastat: A Novel Selective Histone Deacetylase 6 Inhibitor with the Ability to Potentiate Immunotherapy in Melanoma Models. J Med Chem, 63 (18): 10246-10262. [PMID:32815366]

18. Novotny-Diermayr V, Sangthongpitag K, Hu CY, Wu X, Sausgruber N, Yeo P, Greicius G, Pettersson S, Liang AL, Loh YK et al.. (2010) 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, 9 (3): 642-52. [PMID:20197387]

19. Phiel CJ, Zhang F, Huang EY, Guenther MG, Lazar MA, Klein PS. (2001) Histone deacetylase is a direct target of valproic acid, a potent anticonvulsant, mood stabilizer, and teratogen. J Biol Chem, 276 (39): 36734-41. [PMID:11473107]

20. Qian C, Lai CJ, Bao R, Wang DG, Wang J, Xu GX, Atoyan R, Qu H, Yin L, Samson M et al.. (2012) Cancer network disruption by a single molecule inhibitor targeting both histone deacetylase activity and phosphatidylinositol 3-kinase signaling. Clin Cancer Res, 18 (15): 4104-13. [PMID:22693356]

21. Rai M, Soragni E, Chou CJ, Barnes G, Jones S, Rusche JR, Gottesfeld JM, Pandolfo M. (2010) Two new pimelic diphenylamide HDAC inhibitors induce sustained frataxin upregulation in cells from Friedreich's ataxia patients and in a mouse model. PLoS ONE, 5 (1): e8825. [PMID:20098685]

22. Santo L, Hideshima T, Kung AL, Tseng JC, Tamang D, Yang M, Jarpe M, van Duzer JH, Mazitschek R, Ogier WC et al.. (2012) Preclinical activity, pharmacodynamic, and pharmacokinetic properties of a selective HDAC6 inhibitor, ACY-1215, in combination with bortezomib in multiple myeloma. Blood, 119 (11): 2579-89. [PMID:22262760]

23. Shen S, Hadley M, Ustinova K, Pavlicek J, Knox T, Noonepalle S, Tavares MT, Zimprich CA, Zhang G, Robers MB et al.. (2019) Discovery of a New Isoxazole-3-hydroxamate-Based Histone Deacetylase 6 Inhibitor SS-208 with Antitumor Activity in Syngeneic Melanoma Mouse Models. J Med Chem, 62 (18): 8557-8577. [PMID:31414801]

24. Wang C, Schroeder FA, Wey HY, Borra R, Wagner FF, Reis S, Kim SW, Holson EB, Haggarty SJ, Hooker JM. (2014) In vivo imaging of histone deacetylases (HDACs) in the central nervous system and major peripheral organs. J Med Chem, 57 (19): 7999-8009. [PMID:25203558]

25. Yu WC, Yeh TY, Ye CH, Chong PCT, Ho YH, So DK, Yap KY, Peng GR, Shao CH, Jagtap AD et al.. (2023) Discovery of HDAC6, HDAC8, and 6/8 Inhibitors and Development of Cell-Based Drug Screening Models for the Treatment of TGF-β-Induced Idiopathic Pulmonary Fibrosis. J Med Chem, 66 (15): 10528-10557. [PMID:37463500]

26. Zhao C, Zhang Y, Zhang J, Li S, Liu M, Geng Y, Liu F, Chai Q, Meng H, Li M et al.. (2023) Discovery of Novel Fedratinib-Based HDAC/JAK/BRD4 Triple Inhibitors with Remarkable Antitumor Activity against Triple Negative Breast Cancer. J Med Chem, 66 (20): 14150-14174. [PMID:37796543]

How to cite this page

3.5.1.- Histone deacetylases (HDACs): histone deacetylase 1. Last modified on 06/10/2023. Accessed on 16/04/2024. IUPHAR/BPS Guide to PHARMACOLOGY, https://www.guidetomalariapharmacology.org/GRAC/ObjectDisplayForward?objectId=2658.