SMTL ID : 7u59.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Piperidine-4-hydroxamic acid Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: G.335, T.336, E.575, R.664, W.665, G.666 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.336, A:R.664, A:G.666 EDO.2: 4 residues within 4Å: Chain A: N.93, Q.139, N.144, Q.179 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.139, A:N.144, A:Q.179 Water bridges: A:Y.183 EDO.3: 7 residues within 4Å: Chain A: A.2, V.119, R.122, V.124, R.125, A.296, K.298 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.119, A:A.296 Water bridges: A:A.2

1 x LDI: 1-[2-(benzylamino)ethyl]-N-hydroxypiperidine-4-carboxamide(Non-covalent)

LDI.4: 12 residues within 4Å: Chain A: E.24, H.136, H.137, G.145, F.146, D.174, H.176, W.205, D.267, E.274, Y.307 Ligands: ZN.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.146, A:W.205 Hydrogen bonds: A:E.24, A:H.137, A:Y.307 Salt bridges: A:E.274

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: D.174, H.176, D.267 Ligands: LDI.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.174, A:D.174, A:H.176, A:D.267

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:W.196 K.7: 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.2, H2O.5

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

PO4.8: 2 residues within 4Å: Chain A: Q.56, K.106 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.56 Water bridges: A:K.106, A:K.106 Salt bridges: A:K.106 PO4.9: 5 residues within 4Å: Chain A: H.201, N.231, K.232, S.340, E.343 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.343, A:E.343 Water bridges: A:H.201, A:N.231, A:N.231 Salt bridges: A:H.201, A:K.232 PO4.10: 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

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 0 residues within 4Å: (No contacts) 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.24, A:E.24, A:S.89, A:A.94, A:A.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herp, D. et al., First Fluorescent Acetylspermidine Deacetylation Assay for HDAC10 Identifies Selective Inhibitors with Cellular Target Engagement. Chembiochem (2022)

Release Date

2023-01-11

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10