SMTL ID : 7o2p.2 (1 other biounit)

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3756

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x UZW: ~{N}-oxidanyl-4-[(5-thiophen-2-yl-1,2,3,4-tetrazol-1-yl)methyl]benzamide(Non-covalent)

UZW.1: 16 residues within 4Å: Chain A: H.30, P.31, S.98, H.141, G.149, F.150, D.179, H.181, F.210, D.272, L.279, G.310, Y.312 Ligands: ZN.2, IOD.5, GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.150, A:L.279 pi-Stacking: A:F.150, A:H.181, A:F.210

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.140, D.179, H.181, D.272 Ligands: UZW.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.179, A:D.179, A:H.181, A:D.272, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: F.190, D.193, V.196, Y.229 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.190, A:V.196, A:Y.229, H2O.1, H2O.3 K.4: 6 residues within 4Å: Chain A: D.177, D.179, H.181, S.200, L.201, H.202 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.177, A:D.177, A:D.179, A:H.181, A:S.200

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.5: 4 residues within 4Å: Chain A: H.30, S.98, I.99 Ligands: UZW.1 Ligand excluded by PLIP

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: I.10, G.126, V.128, R.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.129 GOL.7: 4 residues within 4Å: Chain A: E.214, N.217, D.219, K.220 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.217, A:K.220 GOL.8: 6 residues within 4Å: Chain A: H.181, A.208, F.209, F.210, L.279 Ligands: UZW.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.181, A:A.208, A:F.210, A:L.279

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

PEG.9: 6 residues within 4Å: Chain A: L.124, T.167, R.168, L.171, E.263, R.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.124, A:R.168 PEG.10: 3 residues within 4Å: Chain A: Y.229, F.360, W.361 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.229, A:Y.229 PEG.11: 3 residues within 4Å: Chain A: K.85, P.86, R.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.87

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

EDO.12: 6 residues within 4Å: Chain A: R.258, A.261, P.262, S.298, L.299, A.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.262, A:A.300

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.13: 7 residues within 4Å: Chain A: Q.187, H.188, E.191, S.213, D.215, K.220, L.223 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.187, A:S.213, A:D.215 Water bridges: A:E.191, A:E.191, A:E.214, A:V.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sandrone, G. et al., Role of Fluorination in the Histone Deacetylase 6 (HDAC6) Selectivity of Benzohydroxamate-Based Inhibitors. Acs Med.Chem.Lett. (2021)

Release Date

2021-10-27

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 6

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