SMTL ID : 6mr5.1 (1 other biounit)

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with a mercaptoacetamide-based inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: W45.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.3: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.2, H2O.3

1 x W45: N-[5-(5,6-dichloro-1H-indol-1-yl)pentyl]-2-sulfanylacetamide(Non-covalent)

W45.4: 15 residues within 4Å: Chain A: H.29, P.30, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, G.309, Y.311 Ligands: ZN.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.149, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:H.140

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 11 residues within 4Å: Chain A: H.181, N.183, H.187, Y.203, F.208, F.209, P.210, N.211, S.212, D.214, A.215 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.208, A:S.212 Water bridges: A:H.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Porter, N.J. et al., Molecular Basis for the Selective Inhibition of Histone Deacetylase 6 by a Mercaptoacetamide Inhibitor. ACS Med Chem Lett (2018)

Release Date

2018-12-05

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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