SMTL ID : 7u8z.3 (3 other biounits)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with fluorinated peptoid inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x M0I: 4-({N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)benzamido}methyl)-3-fluoro-N-hydroxybenzamide(Non-covalent)

M0I.1: 14 residues within 4Å: Chain A: D.26, H.29, P.30, S.97, H.140, G.148, F.149, D.178, H.180, F.209, D.271, G.309, Y.311 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.209 Hydrogen bonds: A:Y.311 Water bridges: A:S.97, A:F.209, A:N.211 pi-Stacking: A:F.149

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.226, Y.228, F.359, W.360 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.228

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: M0I.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.4: 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.6 K.5: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ressing, N. et al., Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia. J.Med.Chem. (2022)

Release Date

2022-11-23

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Hdac6 protein

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