SMTL ID : 3sfh.1

Crystal Structure of Human HDAC8 Inhibitor Complex, an Amino Acid Derived Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 6 residues within 4Å: Chain A: D.177, D.179, H.181, S.200, L.201, H.202 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.181 K.2: 6 residues within 4Å: Chain A: F.190, S.191, T.193, V.196, Y.226, S.227 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:V.196

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.143, D.179, H.181, D.268 Ligands: 1DI.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.179, A:D.179, A:H.181, A:D.268

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 2 residues within 4Å: Chain A: G.108, D.111 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.108 ACT.5: 7 residues within 4Å: Chain A: A.113, I.116, W.142, F.153, C.154, Y.155, L.156 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.116 Hydrogen bonds: A:Y.155, A:L.156 ACT.6: 9 residues within 4Å: Chain A: L.180, D.268, T.269, I.270, D.273, M.275, C.276, S.277, F.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.275, A:C.276, A:S.277, A:F.278, A:F.278

1 x 1DI: (2R)-2-amino-3-(2,4-dichlorophenyl)-1-(1,3-dihydro-2H-isoindol-2-yl)propan-1-one(Non-covalent)

1DI.7: 17 residues within 4Å: Chain A: I.35, R.38, G.141, W.142, H.143, H.144, G.152, F.153, C.154, D.179, H.181, F.209, D.268, G.304, G.305, Y.307 Ligands: ZN.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.209, A:Y.307 Hydrogen bonds: A:G.305 pi-Stacking: A:W.142, A:F.153 Halogen bonds: A:G.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Whitehead, L. et al., Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorg.Med.Chem. (2011)

Release Date

2011-07-20

Peptides

Histone deacetylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 8

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