7U8Z | pdb_00007u8z

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with fluorinated peptoid inhibitor

PDB DOI: https://doi.org/10.2210/pdb7U8Z/pdb

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

Deposited: 2022-03-09 Released: 2022-11-23
Deposition Author(s): Watson, P.R., Cragin, A.D., Christianson, D.W.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.215 (Depositor), 0.215 (DCC)
R-Value Work:
0.172 (Depositor), 0.172 (DCC)
R-Value Observed:
0.174 (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

Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia.

Ressing, N., Schliehe-Diecks, J., Watson, P.R., Sonnichsen, M., Cragin, A.D., Scholer, A., Yang, J., Schaker-Hubner, L., Borkhardt, A., Christianson, D.W., Bhatia, S., Hansen, F.K.

(2022) J Med Chem 65: 15457-15472

PubMed: 36351184 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.2c01418
Primary Citation Related Structures:
7U8Z

PubMed Abstract:
Using a microwave-assisted protocol, we synthesized 16 peptoid-capped HDAC inhibitors (HDACi) with fluorinated linkers and identified two hit compounds. In biochemical and cellular assays, 10h stood out as a potent unselective HDACi with remarkable cytotoxic potential against different therapy-resistant leukemia cell lines. 10h demonstrated prominent antileukemic activity with low cytotoxic activity toward healthy cells. Moreover, 10h exhibited synergistic interactions with the DNA methyltransferase inhibitor decitabine in AML cell lines. The comparison of crystal structures of HDAC6 complexes with 10h and its nonfluorinated counterpart revealed a similar occupation of the L1 loop pocket but slight differences in zinc coordination. The substitution pattern of the acyl residue turned out to be crucial in terms of isoform selectivity. The introduction of an isopropyl group onto the phenyl ring provided the highly HDAC6-selective inhibitor 10p , which demonstrated moderate synergy with decitabine and exceeded the HDAC6 selectivity of tubastatin A.

Organizational Affiliation

Pharmaceutical Institute, Pharmaceutical and Cell Biological Chemistry, University of Bonn, An der Immenburg 4, 53121Bonn, Germany.

Macromolecule Content

Total Structure Weight: 164.26 kDa
Atom Count: 12,433
Modeled Residue Count: 1,426
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A, B, C, D	364	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
M0I Query on M0I Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] SDF format, chain V [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth D]	F [auth A], J [auth B], Q [auth C], V [auth D]	4-({N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)benzamido}methyl)-3-fluoro-N-hydroxybenzamide C₂₆ H₂₇ F N₄ O₄ GBIQEYYBFBGNOZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain V [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth C] Focus chain V [auth D]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain Z [auth D]	Z [auth D]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain Z [auth D] Interactions & Density Focus chain Z [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain S [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth C] mmCIF format, chain AA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain S [auth C]	AA [auth D], G [auth A], N [auth B], S [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain S [auth C] Interactions & Density Focus chain AA [auth D] Focus chain G [auth A] Focus chain N [auth B] Focus chain S [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Y [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth D]	K [auth B] L [auth B] M [auth B] W [auth D] X [auth D] K [auth B], L [auth B], M [auth B], W [auth D], X [auth D], Y [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain T [auth C] SDF format, chain U [auth C] SDF format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] MOL2 format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C] mmCIF format, chain BA [auth D]	BA [auth D] CA [auth D] H [auth A] I [auth A] O [auth B] BA [auth D], CA [auth D], H [auth A], I [auth A], O [auth B], P [auth B], T [auth C], U [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain H [auth A] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain T [auth C] Focus chain U [auth C]