SMTL ID : 6wdx.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Hydroxyethylindole Phenylhydroxamate Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

1 x TWS: N-hydroxy-4-{[3-(2-hydroxyethyl)-1H-indol-1-yl]methyl}benzamide(Non-covalent)

TWS.1: 16 residues within 4Å: Chain A: P.23, E.24, I.27, H.136, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.146, A:F.146, A:F.204, A:W.205, A:W.205 Hydrogen bonds: A:H.137, A:G.305, A:Y.307

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.174, H.176, D.267 Ligands: TWS.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.174, A:D.174, A:H.176, A:D.267

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

PO4.3: 6 residues within 4Å: Chain A: Y.199, H.201, D.212, Y.213, P.229, N.231 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.212, A:Y.213, A:Y.213, A:N.231, A:N.231 Salt bridges: A:H.201 PO4.4: 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:N.231, A:E.343, A:E.343 Salt bridges: A:H.201, A:K.232 PO4.5: 4 residues within 4Å: Chain A: H.43, H.321, K.407, R.408 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.408 Salt bridges: A:H.43, A:H.321

2 x K: POTASSIUM ION(Non-covalent)

K.6: 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:S.195 K.7: 4 residues within 4Å: Chain A: F.185, D.188, V.191, F.224 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.185, A:D.188, A:V.191, H2O.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herbst-Gervasoni, C.J. et al., Structural Basis for the Selective Inhibition of HDAC10, the Cytosolic Polyamine Deacetylase. Acs Chem.Biol. (2020)

Release Date

2020-07-22

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10

Related Entries With Identical Sequence