SMTL ID : 7kbh.3 (2 other biounits)

Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 16)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.68 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.141, D.177, H.179, D.266 Ligands: WB4.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.266

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.224 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:V.194, H2O.1, H2O.2 CA.3: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.175, A:D.177, A:H.179, A:F.199

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

PEG.4: 6 residues within 4Å: Chain A: L.165, K.166, Y.167, H.168, Q.169, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.169

1 x WB4: N-{(1S)-5-{[2-(methylsulfanyl)benzene-1-carbonyl]amino}-1-[5-(naphthalen-2-yl)-1H-imidazol-2-yl]pentyl}-1,3-thiazole-5-carboxamide(Non-covalent)

WB4.5: 22 residues within 4Å: Chain A: G.28, H.29, P.30, M.31, R.35, E.99, D.100, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.207, D.266, L.273, G.302, G.303, G.304 Ligands: ZN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.30, A:L.140, A:F.151, A:F.207, A:F.207 Hydrogen bonds: A:D.100, A:D.100, A:G.150 Water bridges: A:N.96, A:F.207 pi-Stacking: A:H.29, A:F.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, J. et al., Discovery of Highly Selective and Potent HDAC3 Inhibitors Based on a 2-Substituted Benzamide Zinc Binding Group. Acs Med.Chem.Lett. (2020)

Release Date

2020-12-30

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 2

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