6G3O

Crystal structure of human HDAC2 in complex with (R)-6-[3,4-Dioxo-2-(4-trifluoromethoxy-phenylamino)-cyclobut-1-enylamino]-heptanoic acid hydroxyamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Squaramides as novel class I and IIB histone deacetylase inhibitors for topical treatment of cutaneous t-cell lymphoma.

Fournier, J.F.Bhurruth-Alcor, Y.Musicki, B.Aubert, J.Aurelly, M.Bouix-Peter, C.Bouquet, K.Chantalat, L.Delorme, M.Drean, B.Duvert, G.Fleury-Bregeot, N.Gauthier, B.Grisendi, K.Harris, C.S.Hennequin, L.F.Isabet, T.Joly, F.Lafitte, G.Millois, C.Morgentin, R.Pascau, J.Piwnica, D.Rival, Y.Soulet, C.Thoreau, E.Tomas, L.

(2018) Bioorg. Med. Chem. Lett. 28: 2985-2992

  • DOI: 10.1016/j.bmcl.2018.06.029

  • PubMed Abstract: 
  • A series of squaramide-based hydroxamic acids were designed, synthesized and evaluated against human HDAC enzyme. Squaramides were found to be potent in the Hut78 cell line, but initially suffered from low solubility. Leads with improved solubility a ...

    A series of squaramide-based hydroxamic acids were designed, synthesized and evaluated against human HDAC enzyme. Squaramides were found to be potent in the Hut78 cell line, but initially suffered from low solubility. Leads with improved solubility and metabolic profiles were shown to be class I, IIB and IV selective.


    Organizational Affiliation

    Edelris, 115 Avenue Lacassagne, 69003 Lyon, France.,Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France. Electronic address: jean-francois.fournier@umontreal.ca.,Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France.,Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin - BP 48, 91192 Gif-sur-Yvette Cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone deacetylase 2
A, B, C
370Homo sapiensMutation(s): 0 
Gene Names: HDAC2
EC: 3.5.1.98
Find proteins for Q92769 (Homo sapiens)
Go to Gene View: HDAC2
Go to UniProtKB:  Q92769
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
EL8
Query on EL8

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Download CCD File 
A, B, C
(6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide
C18 H20 F3 N3 O5
WFKNHSZTAURQLQ-SNVBAGLBSA-N
 Ligand Interaction
1PE
Query on 1PE

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Download CCD File 
B
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 92.050α = 90.00
b = 93.300β = 90.00
c = 139.420γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Cootmodel building
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references