SMTL ID : 7o2r.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with ITF3985

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x V05: 3,5-bis(fluoranyl)-~{N}-oxidanyl-4-[(5-pyrimidin-2-yl-1,2,3,4-tetrazol-2-yl)methyl]benzamide(Non-covalent)

V05.1: 13 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, G.310, Y.312 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.150, A:F.150 Hydrogen bonds: A:S.98, A:Y.312 pi-Stacking: A:F.150, A:H.181, A:F.210 Halogen bonds: A:S.98

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.140, D.179, H.181, D.272 Ligands: V05.1 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

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

IOD.3: 1 residues within 4Å: Chain A: S.80 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: H.30, S.98 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain A: F.210 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: G.222, L.223 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: Q.295 Ligand excluded by PLIP IOD.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x K: POTASSIUM ION(Non-covalent)

K.9: 4 residues within 4Å: Chain A: F.190, D.193, V.196, Y.229 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.190, A:D.193, A:V.196, A:Y.229, H2O.1 K.10: 5 residues within 4Å: Chain A: D.177, D.179, H.181, S.200, L.201 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 PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain A: E.45, R.48, L.50, S.51 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.45, A:E.45, A:L.50, A:S.51, A:S.51

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
A

Histone deacetylase 6

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