SMTL ID : 5fcw.1 (1 other biounit)

HDAC8 Complexed with a Hydroxamic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x 5YA: 4-naphthalen-1-yl-~{N}-oxidanyl-benzamide(Non-covalent)

5YA.1: 13 residues within 4Å: Chain A: Y.100, D.101, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, G.304, Y.306 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.100, A:D.101, A:F.208, A:F.208, A:F.208 Hydrogen bonds: A:H.143, A:D.178 pi-Stacking: A:F.152, A:F.208

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.267 Ligands: 5YA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.267

1 x K: POTASSIUM ION(Non-covalent)

K.3: 7 residues within 4Å: Chain A: D.176, L.177, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:L.200

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.4: 2 residues within 4Å: Chain A: E.170, K.194 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tabackman, A.A. et al., Structure of 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket. J.Struct.Biol. (2016)

Release Date

2016-10-26

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8

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