6ZW1 | pdb_00006zw1

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with an inhibitor SW101


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 
    0.159 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.140 (Depositor), 0.142 (DCC) 
  • R-Value Observed: 
    0.140 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZW1

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Tetrahydroquinoline-Capped Histone Deacetylase 6 Inhibitor SW-101 Ameliorates Pathological Phenotypes in a Charcot-Marie-Tooth Type 2A Mouse Model.

Shen, S.Picci, C.Ustinova, K.Benoy, V.Kutil, Z.Zhang, G.Tavares, M.T.Pavlicek, J.Zimprich, C.A.Robers, M.B.Van Den Bosch, L.Barinka, C.Langley, B.Kozikowski, A.P.

(2021) J Med Chem 64: 4810-4840

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c02210
  • Primary Citation Related Structures: 
    6ZW1

  • PubMed Abstract: 

    Histone deacetylase 6 (HDAC6) is a promising therapeutic target for the treatment of neurodegenerative disorders. SW-100 ( 1a ), a phenylhydroxamate-based HDAC6 inhibitor (HDAC6i) bearing a tetrahydroquinoline (THQ) capping group, is a highly potent and selective HDAC6i that was shown to be effective in mouse models of Fragile X syndrome and Charcot-Marie-Tooth disease type 2A (CMT2A). In this study, we report the discovery of a new THQ-capped HDAC6i, termed SW-101 ( 1s ), that possesses excellent HDAC6 potency and selectivity, together with markedly improved metabolic stability and druglike properties compared to SW-100 ( 1a ). X-ray crystallography data reveal the molecular basis of HDAC6 inhibition by SW-101 ( 1s ). Importantly, we demonstrate that SW-101 ( 1s ) treatment elevates the impaired level of acetylated α-tubulin in the distal sciatic nerve, counteracts progressive motor dysfunction, and ameliorates neuropathic symptoms in a CMT2A mouse model bearing mutant MFN 2. Taken together, these results bode well for the further development of SW-101 ( 1s ) as a disease-modifying HDAC6i.


  • Organizational Affiliation
    • Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois 60612, United States.

Macromolecule Content 

  • Total Structure Weight: 40.67 kDa 
  • Atom Count: 3,421 
  • Modeled Residue Count: 354 
  • Deposited Residue Count: 359 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone deacetylase 6359Danio rerioMutation(s): 0 
Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio)
Explore F8W4B7 
Go to UniProtKB:  F8W4B7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8W4B7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QRB
(Subject of Investigation/LOI)

Query on QRB



Download:Ideal Coordinates CCD File
C [auth A]1-[[4-(oxidanylcarbamoyl)phenyl]methyl]-3,4-dihydro-2~{H}-quinoline-6-carboxamide
C18 H19 N3 O3
ZRFMDXMQBRKKOA-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
SCN

Query on SCN



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K

Query on K



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free:  0.159 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.140 (Depositor), 0.142 (DCC) 
  • R-Value Observed: 0.140 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.933α = 90
b = 94.158β = 90
c = 51.487γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2021-08-11
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description