SMTL ID : 7sgi.1

Crystal Structure of Danio rerio Histone Deacetylase 10 in Complex with Inhibitor 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x 9DL: 5-[(2-anilino-2-oxoethyl)(methyl)amino]-N-hydroxypentanamide(Non-covalent)

9DL.1: 14 residues within 4Å: Chain A: P.23, E.24, H.136, H.137, G.145, F.146, D.174, H.176, W.205, D.267, E.274, G.305, Y.307 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.24, A:F.146, A:W.205 Hydrogen bonds: A:H.137, A:D.174, A:E.274, A:Y.307 Salt bridges: 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: 9DL.1 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.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:V.191, A:F.224, H2O.2, H2O.3

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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.408 Salt bridges: A:H.43, A:H.321

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

NA.8: 0 residues within 4Å: (No contacts) 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.22, A:E.24, A:A.94, A:A.94, A:A.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Steimbach, R.R. et al., Aza-SAHA Derivatives Are Selective Histone Deacetylase 10 Chemical Probes That Inhibit Polyamine Deacetylation and Phenocopy HDAC10 Knockout. J.Am.Chem.Soc. (2022)

Release Date

2022-10-05

Peptides

Polyamine deacetylase HDAC10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Polyamine deacetylase HDAC10

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