SMTL ID : 6wbw.3 (2 other biounits)

Structure of Human HDAC2 in complex with an ethyl ketone inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x TV1: N-{(1S)-7,7-dihydroxy-1-[5-(2-methoxyquinolin-3-yl)-1H-imidazol-2-yl]nonyl}-1-methylazetidine-3-carboxamide(Non-covalent)

TV1.1: 20 residues within 4Å: Chain A: G.28, H.29, P.30, M.31, E.99, D.100, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.151, A:F.151, A:F.151, A:F.151, A:F.206 Hydrogen bonds: A:D.100, A:D.100, A:H.142 Water bridges: A:F.206

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.177, H.179, D.265, G.302 Ligands: TV1.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.177, A:H.179, A:D.265

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:T.191, A:V.194, H2O.2, H2O.8 CA.4: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.175, A:D.177, A:H.179, A:S.198

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

PEG.5: 5 residues within 4Å: Chain A: L.165, K.166, Y.167, Q.169, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, W. et al., Discovery of ethyl ketone-based HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation. Bioorg.Med.Chem.Lett. (2020)

Release Date

2020-05-06

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 2

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