6TCY

X-ray structure of Danio rerio histone deacetylase 6 (HDAC6) CD2 in complex with a inhibitor SS555

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

  • Deposited: 2019-11-06 Released: 2020-11-04 
  • Deposition Author(s): Stransky, J., Barinka, C.
  • Funding Organization(s): Czech Science Foundation, Czech Academy of Sciences, European Regional Development Fund, Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Rational Design of Suprastat: A Novel Selective Histone Deacetylase 6 Inhibitor with the Ability to Potentiate Immunotherapy in Melanoma Models.

Noonepalle, S.Shen, S.Ptacek, J.Tavares, M.T.Zhang, G.Stransky, J.Pavlicek, J.Ferreira, G.M.Hadley, M.Pelaez, G.Barinka, C.Kozikowski, A.P.Villagra, A.

(2020) J Med Chem 63: 10246-10262

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00567
  • Primary Citation of Related Structures:  
    6TCY

  • PubMed Abstract: 

    Selective inhibition of histone deacetylase 6 (HDAC6) is being recognized as a therapeutic approach for cancers. In this study, we designed a new HDAC6 inhibitor, named Suprastat, using in silico simulations. X-ray crystallography and molecular dynamics simulations provide strong evidence to support the notion that the aminomethyl and hydroxyl groups in the capping group of Suprastat establish significant hydrogen bond interactions, either direct or water-mediated, with residues D460, N530, and S531, which play a vital role in regulating the deacetylase function of the enzyme and which are absent in other isoforms. In vitro characterization of Suprastat demonstrates subnanomolar HDAC6 inhibitory potency and a hundred- to a thousand-fold HDAC6 selectivity over the other HDAC isoforms. In vivo studies reveal that a combination of Suprastat and anti-PD1 immunotherapy enhances antitumor immune response, mediated by a decrease of protumoral M2 macrophages and increased infiltration of antitumor CD8+ effector and memory T-cells.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, District of Columbia 20052, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone deacetylase 6A [auth AAA],
B [auth BBB]
359Danio 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
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N28 (Subject of Investigation/LOI)
Query on N28

Download Ideal Coordinates CCD File 
F [auth AAA],
R [auth BBB]
4-[[[4-(aminomethyl)phenyl]carbamoyl-(4-oxidanylbutyl)amino]methyl]-~{N}-oxidanyl-benzamide
C20 H26 N4 O4
VTRGFHYHEAEHGS-UHFFFAOYSA-N
TOE
Query on TOE

Download Ideal Coordinates CCD File 
L [auth AAA]2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
C7 H16 O4
JLGLQAWTXXGVEM-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth AAA]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
V [auth BBB]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MXE
Query on MXE

Download Ideal Coordinates CCD File 
U [auth BBB]2-METHOXYETHANOL
C3 H8 O2
XNWFRZJHXBZDAG-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth AAA],
O [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth AAA]
H [auth AAA]
I [auth AAA]
J [auth AAA]
K [auth AAA]
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA],
K [auth AAA],
S [auth BBB],
T [auth BBB]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
D [auth AAA],
E [auth AAA],
P [auth BBB],
Q [auth BBB]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
N [auth AAA]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.809α = 90
b = 83.811β = 97.971
c = 86.092γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic15-19640S
Czech Academy of SciencesCzech Republic86652036
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0109
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015043

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description