SMTL ID : 1vkg.1

Crystal Structure of Human HDAC8 complexed with CRA-19156

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.178, L.179, H.180, D.267, G.304 Ligands: CRI.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.178, A:D.178, A:H.180, A:D.267, CRI.3 ZN.4: 8 residues within 4Å: Chain B: H.142, D.178, L.179, H.180, D.267, G.304, Y.306 Ligands: CRI.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.178, B:D.178, B:H.180, B:D.267, CRI.6

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

NA.2: 8 residues within 4Å: Chain A: L.177, D.178, L.179, L.200, H.201, Y.240, T.268, F.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.200 NA.5: 8 residues within 4Å: Chain B: D.176, L.177, D.178, H.180, H.181, S.199, L.200, H.201 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.178, B:L.200, B:L.200

2 x CRI: 5-(4-METHYL-BENZOYLAMINO)-BIPHENYL-3,4'-DICARBOXYLIC ACID 3-DIMETHYLAMIDE-4'-HYDROXYAMIDE(Non-covalent)

CRI.3: 18 residues within 4Å: Chain A: W.141, H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, M.274, G.304, Y.306 Chain B: F.152, P.273, M.274, Y.306 Ligands: ZN.1, CRI.6 11 PLIP interactions: 6 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.152, A:Y.306, B:F.152, B:P.273, B:Y.306, B:Y.306 Hydrogen bonds: A:H.142, A:D.178, A:Y.306 pi-Stacking: A:F.152, B:Y.306 CRI.6: 17 residues within 4Å: Chain A: F.152, P.273, M.274, Y.306 Chain B: H.142, H.143, G.151, F.152, D.178, H.180, F.208, D.267, M.274, G.304, Y.306 Ligands: CRI.3, ZN.4 11 PLIP interactions: 3 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:P.273, A:Y.306, B:F.152, B:F.152, B:F.208 pi-Stacking: A:Y.306, B:F.208 Hydrogen bonds: B:H.142, B:H.143 Water bridges: B:G.304, B:G.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Somoza, J.R. et al., Structural Snapshots of Human HDAC8 Provide Insights into the Class I Histone Deacetylases. Structure (2004)

Release Date

2004-07-27

Peptides

Histone deacetylase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Histone deacetylase 8

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