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

Crystal structure of a HDAC-like protein HDAH from Bordetella sp. with the bound inhibitor ST-17

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.186, H.188, D.274 Ligands: S17.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.186, A:D.186, A:H.188, A:D.274 ZN.6: 5 residues within 4Å: Chain B: H.148, D.186, H.188, D.274 Ligands: S17.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.186, B:D.186, B:H.188, B:D.274 ZN.7: 4 residues within 4Å: Chain B: H.4, H.6, H.64 Ligands: CL.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.4, B:H.6, B:H.64

4 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.184, D.186, H.188, S.207, L.208, H.209 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.184, A:D.184, A:H.188, A:S.207, A:L.208 K.3: 4 residues within 4Å: Chain A: W.197, D.200, V.203, Y.232 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:W.197, A:D.200, A:V.203, H2O.10, H2O.11 K.8: 5 residues within 4Å: Chain B: D.184, D.186, H.188, S.207, L.208 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.184, B:D.184, B:H.188, B:S.207, B:L.208 K.9: 4 residues within 4Å: Chain B: W.197, D.200, V.203, Y.232 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:W.197, B:D.200, B:V.203, H2O.26, H2O.27

2 x S17: methyl 4-bromo-N-[8-(hydroxyamino)-8-oxooctanoyl]-L-phenylalaninate(Non-covalent)

S17.4: 18 residues within 4Å: Chain A: L.27, A.28, I.106, H.148, H.149, F.158, D.186, H.188, F.214, P.216, D.274, G.316, Y.318 Chain B: P.343, Y.344, E.346, F.347 Ligands: ZN.1 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.27, A:I.106, A:F.158, A:F.158, A:F.214, A:F.214, A:F.214, B:F.347, B:F.347 Hydrogen bonds: A:H.149 Water bridges: A:Y.318, A:Y.318 pi-Stacking: B:F.347 S17.10: 19 residues within 4Å: Chain A: P.343, Y.344, E.346, F.347 Chain B: L.27, A.28, I.106, H.148, H.149, F.158, D.186, H.188, F.214, P.216, D.274, L.281, G.316, Y.318 Ligands: ZN.6 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:E.346, A:F.347, A:F.347, B:L.27, B:I.106, B:I.106, B:F.158, B:F.158, B:F.158, B:F.214, B:F.214, B:L.281 pi-Stacking: A:F.347 Hydrogen bonds: B:H.149 Water bridges: B:Y.318, B:Y.318

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain B: M.1, H.64, V.337 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.64

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 6 residues within 4Å: Chain B: H.4, H.5, H.6, H.64, V.337 Ligands: ZN.7 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schaefer, S. et al., Phenylalanine-Containing Hydroxamic Acids as Selective Inhibitors of Class Iib Histone Deacetylases (Hdacs). Bioorg.Med.Chem. (2008)

Release Date

2008-01-08

Peptides

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

HISTONE DEACETYLASE-LIKE AMIDOHYDROLASE

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