Coordinate files and representative results for docking of HDACs with phorbazole analogues

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Guillaume Axel Petit; Ida Amalie Nysted Reierth; Jeanette Hammer Andersen, 2025, "Coordinate files and representative results for docking of HDACs with phorbazole analogues", https://doi.org/10.18710/3DNRGM, DataverseNO, V1

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Description	This data represent the structural coordinates, in mol2 file format, of the HDAC models and of the phorbazole compounds used to generate the docking results presented in the article "Investigation of the Histone Deacetylase Inhibitor Potential of Phorbazole Analogues" By IA Nysted Reierth et al. (see related publication section). The analysis was perform using "ensemble docking" with the GOLD software from CCDC (see method section of the paper for more details). HDAC structures were grouped based on their class (I or II) and the docking was performed separately for each group. The result folder contains the best ranking pose for each compound against each of the class 1 and 2 HDAC models. The bestranking.lst file is a summary of the GOLD score for these compounds. A "pymol session" file, HDAC_class*_dockingresults.pse also summarise these results for visualisation with Pymol. The pose can be opened together with the prepared structures for analysis and visualisation. The files might be best viewed in "tree" representation from the main page to get a better idea of the folder structure. This dataset is related to dataset "https://doi.org/10.18710/WUJCYB, Molecular dynamic trajectories for HDAC9 binding analysis", where the docking results presented here are further explored through molecular dynamic simulations. (2025-04-29)
Subject	Chemistry; Medicine, Health and Life Sciences; Computer and Information Science
Keyword	Docking, GOLD docking software, Drug discovery, HDAC, HDAC inhibitor
Related Publication	Is Supplement To: Ida Amalie Nystad Reierth, Yngve Guttormsen, Jeanette H. Andersen, Espen H. Hansen, Ahmed Mossad Abdelhady, Manuel K. Langer, Bengt Erik Haug, Annette Bayer, Guillaume A. Petit (2026). Investigation of the histone deacetylase inhibitor potential of phorbazole analogues. Bioorganic & Medicinal Chemistry, 133:118489. https://doi.org/10.1016/j.bmc.2025.118489doi: 10.1016/j.bmc.2025.118489
License/Data Use Agreement	CC0 1.0

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	00_README.txt Plain Text - 7.5 KB Published Nov 28, 2025 0 Downloads MD5: 283829c87faa6778a32089132fad34a2 Read me file documentation of the data set	Preview "00_README.txt" Access File File Access Public Download Options Plain Text Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_01.mol2 compound/Unknown - 2.9 KB Published Nov 28, 2025 0 Downloads MD5: db6bdc45c9b53070e4b6af9151779ca2	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_02.mol2 compound/Unknown - 2.9 KB Published Nov 28, 2025 0 Downloads MD5: ab77f028ebb8d8669e0b76479697b3b0	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_03.mol2 compound/Unknown - 4.5 KB Published Nov 28, 2025 0 Downloads MD5: 347290d268c77a11cab3250b4cdff369	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_04.mol2 compound/Unknown - 4.5 KB Published Nov 28, 2025 0 Downloads MD5: 0a5936493e4077a5cef4b76992ac4aac	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
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	compound_06.mol2 compound/Unknown - 3.2 KB Published Nov 28, 2025 0 Downloads MD5: 4521386c7f3be490dd00b95e3020c358	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_07.mol2 compound/Unknown - 2.8 KB Published Nov 28, 2025 0 Downloads MD5: 28833b21286e31876929b4b4410354ac	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_09.mol2 compound/Unknown - 3.0 KB Published Nov 28, 2025 0 Downloads MD5: d9d780efdec3363bcc0228fab926f0aa	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX
	compound_10a.mol2 compound/Unknown - 3.5 KB Published Nov 28, 2025 0 Downloads MD5: 1e2a0e6ce0806d4624144394f1bda683	Access File File Access Public Download Options Original File Format Download Metadata Data File Citation Download EndNote XML Download RIS Download BibTeX

Citation Metadata

Persistent Identifier	doi:10.18710/3DNRGM
Publication Date	2025-11-28
Title	Coordinate files and representative results for docking of HDACs with phorbazole analogues
Author	UiT The Arctic University of Norway0000-0002-8251-0754 UiT The Arctic University of Norway0009-0005-1893-5925 UiT The Arctic University of Norway0000-0002-6059-060X
Point of Contact	Use email button above to contact. Petit Guillaume (UiT The Arctic University of Norway) Ida Amalie Nysted Reierth (UiT The Arctic University of Norway) Jeanette Hammer Andersen (UiT The Arctic University of Norway)
Description	This data represent the structural coordinates, in mol2 file format, of the HDAC models and of the phorbazole compounds used to generate the docking results presented in the article "Investigation of the Histone Deacetylase Inhibitor Potential of Phorbazole Analogues" By IA Nysted Reierth et al. (see related publication section). The analysis was perform using "ensemble docking" with the GOLD software from CCDC (see method section of the paper for more details). HDAC structures were grouped based on their class (I or II) and the docking was performed separately for each group. The result folder contains the best ranking pose for each compound against each of the class 1 and 2 HDAC models. The bestranking.lst file is a summary of the GOLD score for these compounds. A "pymol session" file, HDAC_class*_dockingresults.pse also summarise these results for visualisation with Pymol. The pose can be opened together with the prepared structures for analysis and visualisation. The files might be best viewed in "tree" representation from the main page to get a better idea of the folder structure. This dataset is related to dataset "https://doi.org/10.18710/WUJCYB, Molecular dynamic trajectories for HDAC9 binding analysis", where the docking results presented here are further explored through molecular dynamic simulations. (2025-04-29)
Subject	Chemistry; Medicine, Health and Life Sciences; Computer and Information Science
Keyword	Docking (Molecular Docking Simulation) https://meshb.nlm.nih.gov/record/ui?ui=D062105 GOLD docking software Drug discovery (Drug Discovery) https://meshb.nlm.nih.gov/record/ui?ui=D055808 HDAC (Histone Deacetylases) https://meshb.nlm.nih.gov/record/ui?ui=D006655 HDAC inhibitor (Histone Deacetylase Inhibitors) https://meshb.nlm.nih.gov/record/ui?ui=D056572
Related Publication	Is Supplement To: Ida Amalie Nystad Reierth, Yngve Guttormsen, Jeanette H. Andersen, Espen H. Hansen, Ahmed Mossad Abdelhady, Manuel K. Langer, Bengt Erik Haug, Annette Bayer, Guillaume A. Petit (2026). Investigation of the histone deacetylase inhibitor potential of phorbazole analogues. Bioorganic & Medicinal Chemistry, 133:118489. https://doi.org/10.1016/j.bmc.2025.118489 doi 10.1016/j.bmc.2025.118489 https://doi.org/10.1016/j.bmc.2025.118489 Is Supplement To: Investigation of the Histone Deacetylase Inhibitor Potential of Phorbazole Analogues, Ida Amalie Nystad Reierth#, Yngve Guttormsen#, Jeanette H. Andersen, Espen H. Hansen, Ahmed Mossad Abdelhady, Manuel K. Langer, Bengt Erik Haug, Annette Bayer, Guillaume A. Petit, Preprint doi: https://dx.doi.org/10.2139/ssrn.5208099 doi 10.2139/ssrn.5208099 https://dx.doi.org/10.2139/ssrn.5208099
Language	English
Producer	UiT The Arctic University of Norway (Marbio) (UiT) https://en.uit.no/
Production Date	2024-02-07
Production Location	Tromsø, UiT, Marbio
Contributor	Data Collector: Ida Amalie Nysted Reierth Project Leader: Guillaume A. Petit Project Manager: Jeanette H. Andersen
Funding Information	UiT: UiT pilot grant
Distributor	UiT The Arctic University of Norway (UiT) https://dataverse.no/dataverse/uit
Depositor	Petit, Guillaume
Deposit Date	2025-04-30
Date of Collection	Start Date: 2024-02-07
Data Type	Computational data; Molecular coordinates
Software	GOLD, Version: v2023.2.0 Pymol, Version: 2.5.7
Related Material	The HDAC model structures used in this study were downloaded from the protein databank: 1T64: https://doi.org/10.2210/pdb1T64/pdb 3SFF: https://doi.org/10.2210/pdb3SFF/pdb 4LY1: https://doi.org/10.2210/pdb4LY1/pdb 4A69: https://doi.org/10.2210/pdb4A69/pdb 5ICN: https://doi.org/10.2210/pdb5ICN/pdb 5VI6: https://doi.org/10.2210/pdb5VI6/pdb 6WBZ: https://doi.org/10.2210/pdb6WBZ/pdb 7KBG: https://doi.org/10.2210/pdb7KBG/pdb 7ZZP: https://doi.org/10.2210/pdb7ZZP/pdb 2VQQ: https://doi.org/10.2210/pdb2VQQ/pdb 3C10: https://doi.org/10.2210/pdb3C10/pdb 3ZNR: https://doi.org/10.2210/pdb3ZNR/pdb 5EDU: https://doi.org/10.2210/pdb5EDU/pdb
Related Dataset	Molecular dynamic trajectories for HDAC9 binding analysis: https://doi.org/10.18710/WUJCYB

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