SMTL ID : 6g3o.1 (2 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.27 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.171, H.173, D.259 Ligands: EL8.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.171, A:H.173, A:D.259

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.169, D.171, H.173, S.192, F.193, H.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.169, A:D.169, A:D.171, A:H.173, A:F.193

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: F.182, T.185, V.188, Y.217 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.188

1 x EL8: (6~{R})-6-[[3,4-bis(oxidanylidene)-2-[[4-(trifluoromethyloxy)phenyl]amino]cyclobuten-1-yl]amino]-~{N}-oxidanyl-heptanamide(Non-covalent)

EL8.4: 16 residues within 4Å: Chain A: Q.21, G.22, H.23, P.24, D.94, H.135, H.136, G.144, F.145, D.171, H.173, F.200, D.259, L.266, Y.298 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.145, A:F.200, A:F.200, A:F.200 Hydrogen bonds: A:D.94, A:D.94, A:G.144 pi-Stacking: A:H.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fournier, J.F. et al., Squaramides as novel class I and IIB histone deacetylase inhibitors for topical treatment of cutaneous t-cell lymphoma. Bioorg. Med. Chem. Lett. (2018)

Release Date

2018-06-27

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 2

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