6VNQ

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor

PDB DOI: https://doi.org/10.2210/pdb6VNQ/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-01-29 Released: 2020-05-13
Deposition Author(s): Herbst-Gervasoni, C.J., Christianson, D.W.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.231
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation 3D Report Full Report

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

Literature

Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors.

Morgen, M., Steimbach, R.R., Geraldy, M., Hellweg, L., Sehr, P., Ridinger, J., Witt, O., Oehme, I., Herbst-Gervasoni, C.J., Osko, J.D., Porter, N.J., Christianson, D.W., Gunkel, N., Miller, A.K.

(2020) ChemMedChem 15: 1163-1174

PubMed: 32348628 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cmdc.202000149
Primary Citation of Related Structures:
6VNQ, 6VNR

PubMed Abstract:
We report the synthesis and evaluation of a class of selective multitarget agents for the inhibition of HDAC6, HDAC8, and HDAC10. The concept for this study grew out of a structural analysis of the two selective inhibitors Tubastatin A (HDAC6/10) and PCI-34051 (HDAC8), which we recognized share the same N-benzylindole core. Hybridization of the two inhibitor structures resulted in dihydroxamic acids with benzyl-indole and -indazole core motifs. These substances exhibit potent activity against HDAC6, HDAC8, and HDAC10, while retaining selectivity over HDAC1, HDAC2, and HDAC3. The best substance inhibited the viability of the SK-N-BE(2)C neuroblastoma cell line with an IC ₅₀ value similar to a combination treatment with Tubastatin A and PCI-34051. This compound class establishes a proof of concept for such hybrid molecules and could serve as a starting point for the further development of enhanced HDAC6/8/10 inhibitors.

Organizational Affiliation

Cancer Drug Development Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany.

Macromolecule Content

Total Structure Weight: 75.84 kDa
Atom Count: 5,210
Modelled Residue Count: 638
Deposited Residue Count: 676
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyamine deacetylase HDAC10	A	676	Danio rerio	Mutation(s): 2 Gene Names: hdac10 EC: 3.5.1.48 (PDB Primary Data), 3.5.1.62 (PDB Primary Data)
UniProt
Find proteins for F1QCV2 (Danio rerio) Explore F1QCV2 Go to UniProtKB: F1QCV2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1QCV2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
R5G (Subject of Investigation/LOI) Query on R5G Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide C₁₇ H₁₅ N₃ O₄ IRJZGNPPEWBPKI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A]	H [auth A], I [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.231
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.549	α = 90
b = 80.549	β = 90
c = 245.37	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Herbst-Gervasoni, C.J.

Christianson, D.W.

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM49758

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2020-07-15
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description