SMTL ID : 5ix0.1 (3 other biounits)

HDAC2 WITH LIGAND BRD7232

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.171, H.173, D.259 Ligands: 6EZ.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.171, A:D.171, A:H.173, A:D.259

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.169, D.171, H.173, S.192, F.193, H.194 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.169, A:D.169, A:D.171, A:H.173, A:F.193 CA.3: 4 residues within 4Å: Chain A: F.182, T.185, V.188, Y.217 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.182, A:T.185, A:V.188, H2O.3, H2O.3

1 x 6EZ: (3-exo)-N-(4-amino-4'-fluoro[1,1'-biphenyl]-3-yl)-8-oxabicyclo[3.2.1]octane-3-carboxamide(Non-covalent)

6EZ.4: 20 residues within 4Å: Chain A: Y.19, M.25, R.29, F.104, G.133, L.134, H.135, H.136, G.144, F.145, C.146, D.171, H.173, F.200, D.259, L.266, G.295, G.296, Y.298 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.134, A:L.134, A:L.134, A:F.145, A:F.145, A:F.145, A:F.200, A:L.266 Hydrogen bonds: A:H.136, A:G.144, A:Y.298

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

PEG.5: 4 residues within 4Å: Chain A: G.15, Y.18, H.28, Y.331 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.28, A:Y.331 PEG.6: 5 residues within 4Å: Chain A: L.159, K.160, Y.161, Q.163, R.187 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.163, A:R.187

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

PG4.7: 4 residues within 4Å: Chain A: R.301, E.330, Y.331, G.333 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.265, A:R.265, A:R.265, A:R.265

1 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.8: 4 residues within 4Å: Chain A: D.13, N.16, Y.17, D.99 No protein-ligand interaction detected (PLIP)

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 4 residues within 4Å: Chain A: K.61, Y.62, A.181, R.187 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.187 Water bridges: A:K.61, A:R.187 PGE.10: 8 residues within 4Å: Chain A: Q.163, R.164, D.186, Y.217, M.246, Y.247, Q.248, P.369 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.163

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
A

Histone deacetylase 2

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