SMTL ID : 7u3m.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with N-methylpiperazine Benzhydroxamic Acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x L8C: N-hydroxy-4-[(4-methylpiperazin-1-yl)methyl]benzamide(Non-covalent)

L8C.1: 15 residues within 4Å: Chain A: E.24, I.27, A.94, H.137, G.145, F.146, D.174, H.176, F.204, W.205, D.267, E.274, G.305, Y.307 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.27, A:F.146, A:W.205 Hydrogen bonds: A:H.176, A:Y.307 Salt bridges: A:E.24, A:E.24, A:E.274, A:E.274

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.174, H.176, D.267 Ligands: L8C.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.174, A:D.174, A:H.176, A:D.267, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.172, D.174, H.176, S.195, W.196 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.172, A:D.172, A:D.174, A:H.176, A:W.196 K.4: 4 residues within 4Å: Chain A: F.185, D.188, V.191, F.224 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.185, A:D.188, A:V.191, H2O.3, H2O.4

3 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: Y.199, H.201, D.212, Y.213, P.229, N.231 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.213, A:N.231, A:N.231, A:N.231 Water bridges: A:Y.213, A:N.347 Salt bridges: A:H.201 PO4.6: 5 residues within 4Å: Chain A: H.201, N.231, K.232, S.340, E.343 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.340, A:E.343 Water bridges: A:N.231 Salt bridges: A:H.201, A:K.232 PO4.7: 4 residues within 4Å: Chain A: H.43, H.321, K.407, R.408 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.408 Water bridges: A:H.43 Salt bridges: A:H.43, A:H.321

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zeyen, P. et al., Identification of histone deacetylase 10 (HDAC10) inhibitors that modulate autophagy in transformed cells. Eur.J.Med.Chem. (2022)

Release Date

2022-04-06

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10

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