6G3O

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

PDB DOI: https://doi.org/10.2210/pdb6G3O/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2018-03-26 Released: 2018-06-27
Deposition Author(s): Isabet, T., Aurelly, M., Chantalat, L., Thoreau, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.219
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

PubMed: 30122227 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2018.06.029
Primary Citation of Related Structures:
6G3O

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 and metabolic profiles were shown to be class I, IIB and IV selective.

Organizational Affiliation

Nestlé Skin Health R&D, 2400 Route des colles, BP 87, 06902 Sophia-Antipolis Cedex, France. Electronic address: jean-francois.fournier@umontreal.ca.

Macromolecule Content

Total Structure Weight: 129.53 kDa
Atom Count: 9,438
Modelled Residue Count: 1,101
Deposited Residue Count: 1,110
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone deacetylase 2	A, B, C	370	Homo sapiens	Mutation(s): 0 Gene Names: HDAC2 EC: 3.5.1.98
UniProt & NIH Common Fund Data Resources
Find proteins for Q92769 (Homo sapiens) Explore Q92769 Go to UniProtKB: Q92769
PHAROS: Q92769 GTEx: ENSG00000196591
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92769
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EL8 Query on EL8 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C]	G [auth A], K [auth B], R [auth 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		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain R [auth C]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B]	N [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain S [auth C]	M [auth B], S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain M [auth B] Focus chain S [auth C] Interactions & Density Focus chain M [auth B] Focus chain S [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain O [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain O [auth C]	D [auth A], H [auth B], O [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain O [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain O [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain P [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain P [auth C]	E [auth A], I [auth B], P [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain P [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C]	F [auth A], J [auth B], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain Q [auth C]