SMTL ID : 8cj7.2 (2 other biounits)

HDAC6 selective degraded (difluoromethyl)-1,3,4-oxadiazole substrate inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 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.178, A:H.180, A:S.199, A:L.200 K.2: 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.1, H2O.6

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: UTO.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

1 x UTO: 6-[(5-pyridin-2-yl-1,2$l^{4},3,4-tetrazacyclopenta-1,3-dien-2-yl)methyl]pyridine-3-carbohydrazide(Non-covalent)

UTO.4: 15 residues within 4Å: Chain A: D.26, H.29, P.30, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, Y.311 Ligands: ZN.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.97, A:G.148, A:Y.311, A:Y.311 pi-Stacking: A:F.149, A:F.209 pi-Cation interactions: A:H.29

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

IOD.5: 4 residues within 4Å: Chain A: E.44, R.47, L.49, S.50 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ripa, L. et al., Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism. J.Med.Chem. (2023)

Release Date

2023-10-18

Peptides

Histone deacetylase 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 6

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