SMTL ID : 2v5x.1 (1 other biounit)

Crystal structure of HDAC8-inhibitor complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.178, H.180, D.267, G.304 Ligands: V5X.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.178, A:H.180, A:D.267

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.176, 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:H.180, A:S.199, A:L.200 K.3: 5 residues within 4Å: Chain A: F.189, T.192, V.195, Y.225, S.226 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:T.192, A:V.195, A:Y.225, H2O.3, H2O.4

1 x V5X: (2R)-N~8~-HYDROXY-2-{[(5-METHOXY-2-METHYL-1H-INDOL-3-YL)ACETYL]AMINO}-N~1~-[2-(2-PHENYL-1H-INDOL-3-YL)ETHYL]OCTANEDIAMIDE(Non-covalent)

V5X.4: 17 residues within 4Å: Chain A: D.101, H.142, H.143, G.151, F.152, D.178, H.180, F.207, F.208, P.209, G.210, D.267, P.273, M.274, G.304, Y.306 Ligands: ZN.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.152, A:F.152, A:F.152, A:F.208, A:F.208 Hydrogen bonds: A:D.101, A:D.101, A:H.143, A:Y.306 Water bridges: A:F.208, A:Q.263, A:Q.263 pi-Stacking: A:F.208, A:F.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vannini, A. et al., Substrate Binding to Histone Deacetylases as Revealed by Crystal Structure of Hdac8-Substrate Complex. Embo Rep. (2007)

Release Date

2007-09-04

Peptides

HISTONE DEACETYLASE 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HISTONE DEACETYLASE 8

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