SMTL ID : 6vnq.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Bishydroxamic Acid Based Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x R5G: N-hydroxy-1-{[4-(hydroxycarbamoyl)phenyl]methyl}-1H-indole-6-carboxamide(Non-covalent)

R5G.1: 16 residues within 4Å: Chain A: E.24, C.25, N.93, A.94, H.136, H.137, G.145, F.146, D.174, H.176, W.205, D.267, E.274, G.305, Y.307 Ligands: ZN.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.24, A:A.94, A:F.146, A:F.146, A:F.146, A:W.205, A:Y.307 Hydrogen bonds: A:N.93, A:H.137, A:Y.307 pi-Cation interactions: A:H.176

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

EDO.2: 2 residues within 4Å: Chain A: H.201 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.232, A:K.232 EDO.3: 3 residues within 4Å: Chain A: V.35, E.38, A.39 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.35

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.174, H.176, D.267 Ligands: R5G.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.5: 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.6: 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:V.191, A:F.224, H2O.3, H2O.7

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

PO4.7: 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:Y.213, A:N.231, A:N.231, A:N.231 Water bridges: A:N.347 Salt bridges: A:H.201 PO4.8: 6 residues within 4Å: Chain A: H.201, N.231, K.232, S.340, E.343 Ligands: EDO.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.340 Water bridges: A:N.231, A:K.232, A:K.232 Salt bridges: A:H.201, A:K.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morgen, M. et al., Design and Synthesis of Dihydroxamic Acids as HDAC6/8/10 Inhibitors. Chemmedchem (2020)

Release Date

2020-05-13

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10

Related Entries With Identical Sequence