SMTL ID : 6thv.1

X-ray structure of the Danio rerio histone deacetylase 6 (HDAC6; catalytic domain 2) in complex with Tubastatin A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.173, H.175, D.266 Ligands: N9W.13 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:D.173, A:H.175, A:D.266, H2O.1

3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.2: 5 residues within 4Å: Chain A: D.171, D.173, H.175, S.194, L.195 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.171, A:D.173, A:H.175, A:S.194, A:L.195 K.3: 4 residues within 4Å: Chain A: F.184, D.187, V.190, Y.223 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.184, A:D.187, A:V.190, A:Y.223, H2O.4 K.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: H.245, P.249, L.348, L.358 Ligands: PEG.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.245 EDO.5: 5 residues within 4Å: Chain A: F.243, H.244, M.248, R.252, Q.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.252, A:R.252 Water bridges: A:Q.289, A:Q.289

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

PEG.6: 7 residues within 4Å: Chain A: N.18, D.21, H.24, S.92, I.93, F.94, F.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.18, A:D.21, A:S.92 PEG.7: 4 residues within 4Å: Chain A: P.249, R.252, S.357 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.253, A:S.357, A:S.357 Water bridges: A:R.252

2 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.8: 3 residues within 4Å: Chain A: W.20, R.81, N.84 No protein-ligand interaction detected (PLIP) SCN.9: 7 residues within 4Å: Chain A: Q.181, E.185, K.214, V.215, G.216, L.217, N.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.216 Water bridges: A:E.185

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

NA.10: 3 residues within 4Å: Chain A: R.53, N.112, Q.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.53 Water bridges: A:R.53, A:Q.115

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 5 residues within 4Å: Chain A: R.221, G.222, Y.223, F.354, W.355 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.221 Water bridges: A:Y.223

1 x N9W: 4-[(2-methyl-3,4-dihydro-1~{H}-pyrido[4,3-b]indol-5-yl)methyl]-~{N}-oxidanyl-benzamide(Non-covalent)

N9W.13: 13 residues within 4Å: Chain A: P.25, S.92, H.135, G.143, F.144, D.173, H.175, F.204, D.266, L.273, G.304, Y.306 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.25, A:F.144, A:F.204, A:F.204, A:L.273, A:L.273 Hydrogen bonds: A:H.175, A:Y.306 pi-Stacking: A:F.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, S. et al., Structural and in Vivo Characterization of Tubastatin A, a Widely Used Histone Deacetylase 6 Inhibitor. Acs Med.Chem.Lett. (2020)

Release Date

2020-07-15

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 6

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