SMTL ID : 5iwg.2 (2 other biounits)

HDAC2 WITH LIGAND BRD4884

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.170, H.172, D.258 Ligands: IWX.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.170, A:D.170, A:H.172, A:D.258

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.168, D.170, H.172, S.191, F.192, H.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.168, A:D.168, A:D.170, A:H.172, A:S.191 CA.4: 4 residues within 4Å: Chain A: F.181, T.184, V.187, Y.216 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.181, A:T.184, A:V.187, A:Y.216, H2O.4

1 x IWX: N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)oxane-4-carboxamide(Non-covalent)

IWX.3: 20 residues within 4Å: Chain A: Y.18, M.24, R.28, F.103, G.132, L.133, H.134, H.135, G.143, F.144, C.145, D.170, H.172, F.199, D.258, L.265, G.294, G.295, Y.297 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.133, A:L.133, A:L.133, A:F.144, A:F.199, A:L.265 Hydrogen bonds: A:H.135, A:G.143, A:Y.297

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: K.273, N.320, H.338 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.273, A:N.320 Water bridges: A:E.317, A:E.317, A:E.317, A:H.338 PEG.6: 4 residues within 4Å: Chain A: D.12, N.15, Y.16, D.98 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.12 PEG.7: 3 residues within 4Å: Chain A: E.329, Y.330, G.332 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.300

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 2 residues within 4Å: Chain A: N.343, T.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.343, A:T.345

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, F.F. et al., Kinetic and structural insights into the binding of histone deacetylase 1 and 2 (HDAC1, 2) inhibitors. Bioorg.Med.Chem. (2016)

Release Date

2016-08-31

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 2

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