6DVL

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-115

PDB DOI: https://doi.org/10.2210/pdb6DVL/pdb

Classification: hydrolase/hydrolase inhibitor
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-06-24 Released: 2018-08-29
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: 2.10 Å
R-Value Free: 0.203
R-Value Work: 0.176
R-Value Observed: 0.177

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.

Porter, N.J., Osko, J.D., Diedrich, D., Kurz, T., Hooker, J.M., Hansen, F.K., Christianson, D.W.

(2018) J Med Chem 61: 8054-8060

PubMed: 30118224 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acs.jmedchem.8b01013
Primary Citation of Related Structures:
6DVL, 6DVM, 6DVN, 6DVO

PubMed Abstract:
Four crystal structures are presented of histone deacetylase 6 (HDAC6) complexes with para-substituted phenylhydromaxamate inhibitors, including bulky peptoids. These structures provide insight regarding the design of capping groups that confer selectivity for binding to HDAC6, specifically with regard to interactions in a pocket formed by the L1 loop. Capping group interactions may also influence hydroxamate-Zn ²⁺ coordination with monodentate or bidentate geometry.

Organizational Affiliation

Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States.

Macromolecule Content

Total Structure Weight: 81.73 kDa
Atom Count: 6,037
Modelled Residue Count: 711
Deposited Residue Count: 728
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F8W4B7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HBG Query on HBG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B]	F [auth A], J [auth B]	N-[2-(cyclohexylamino)-2-oxoethyl]-N-{[4-(hydroxycarbamoyl)phenyl]methyl}-3,5-dimethylbenzamide C₂₅ H₃₁ N₃ O₄ PEXKZGDNGWXGSQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
HBG	Binding MOAD: 6DVL	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.203
R-Value Work: 0.176
R-Value Observed: 0.177
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.982	α = 90
b = 82.601	β = 98.49
c = 88.91	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-08-29

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: 2018-08-29
Type: Initial release
Version 1.1: 2018-09-26
Changes: Data collection, Database references
Version 1.2: 2019-12-18
Changes: Author supporting evidence
Version 1.3: 2023-10-11
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description