7O2P | pdb_00007o2p

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3756

PDB DOI: https://doi.org/10.2210/pdb7O2P/pdb

Classification: HYDROLASE
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-03-31 Released: 2021-10-27
Deposition Author(s): Zrubek, K., Sandrone, G., Cukier, C.D., Stevenazzi, A.
Funding Organization(s): European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.261 (Depositor), 0.246 (DCC)
R-Value Work:
0.195 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors.

Sandrone, G., Cukier, C.D., Zrubek, K., Marchini, M., Vergani, B., Caprini, G., Fossati, G., Steinkuhler, C., Stevenazzi, A.

(2021) ACS Med Chem Lett 12: 1810-1817

PubMed: 34795871 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.1c00425
Primary Citation Related Structures:
7O2P, 7O2R

PubMed Abstract:
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.

Organizational Affiliation

Research & Development, Italfarmaco Group, Via dei Lavoratori 54, Cinisello Balsamo, Milan I-20092, Italy.

Macromolecule Content

Total Structure Weight: 83.44 kDa
Atom Count: 5,925
Modeled Residue Count: 713
Deposited Residue Count: 730
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 6	A, B	365	Danio rerio	Mutation(s): 0 Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7 Go to UniProtKB: F8W4B7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F8W4B7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UZW (Subject of Investigation/LOI) Query on UZW Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain O [auth B] MOL2 format, chain C [auth A] MOL2 format, chain O [auth B] mmCIF format, chain C [auth A] mmCIF format, chain O [auth B]	C [auth A], O [auth B]	~{N}-oxidanyl-4-[(5-thiophen-2-yl-1,2,3,4-tetrazol-1-yl)methyl]benzamide C₁₃ H₁₁ N₅ O₂ S UFUGFWWXDWPEQE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain O [auth B] Interactions & Density Focus chain C [auth A] Focus chain O [auth B]
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain AA [auth B]	AA [auth B]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₁₁ H₂₆ N₂ O₆ HHKZCCWKTZRCCL-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Interactions & Density Focus chain AA [auth B]
IOD Query on IOD Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain N [auth A] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B]	G [auth A], H [auth A], N [auth A], S [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth A] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth A] Focus chain S [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain K [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain K [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	K [auth A], W [auth B], X [auth B], Y [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain K [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	I [auth A], J [auth A], T [auth B], U [auth B], V [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth B]	D [auth A], P [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Z [auth B]	L [auth A], M [auth A], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain Z [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	E [auth A], F [auth A], Q [auth B], R [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain Q [auth B] Focus chain R [auth B]