6MR5 | pdb_00006mr5

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitor

PDB DOI: https://doi.org/10.2210/pdb6MR5/pdb

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

Deposited: 2018-10-11 Released: 2018-12-05
Deposition Author(s): Porter, N.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: 1.85 Å
R-Value Free:
0.226 (Depositor), 0.242 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Molecular Basis for the Selective Inhibition of Histone Deacetylase 6 by a Mercaptoacetamide Inhibitor.

Porter, N.J., Shen, S., Barinka, C., Kozikowski, A.P., Christianson, D.W.

(2018) ACS Med Chem Lett 9: 1301-1305

PubMed: 30613344 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.8b00487
Primary Citation Related Structures:
6MR5

PubMed Abstract:
Mercaptoacetamide histone deacetylase inhibitors are neuroprotective agents that do not exhibit the genotoxicity associated with more commonly used hydroxamate inhibitors. Here, we present the crystal structure of a selective mercaptoacetamide complexed with the C-terminal catalytic domain of HDAC6. When compared with the structure of a mercaptoacetamide bound to the class I isozyme HDAC8, different interactions are observed with the conserved tandem histidine pair in the active site. These differences likely contribute to the selectivity for inhibition of HDAC6, an important target for cancer chemotherapy and the treatment of neurodegenerative disease.

Organizational Affiliation

Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, United States.

Macromolecule Content

Total Structure Weight: 82.01 kDa
Atom Count: 5,942
Modeled Residue Count: 711
Deposited Residue Count: 728
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	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
W45 (Subject of Investigation/LOI) Query on W45 Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide C₁₅ H₁₈ Cl₂ N₂ O S MHKHGVSRGWQPII-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain K [auth B]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], I [auth B], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.226 (Depositor), 0.242 (DCC)
R-Value Work: 0.190 (Depositor)
R-Value Observed: 0.192 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.01	α = 90
b = 46.46	β = 119.19
c = 96.4	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-05

Deposition Author(s):

Porter, N.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: 2018-12-05
Type: Initial release
Version 1.1: 2019-01-23
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations