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

Structure of HDAC2 in complex with an inhibitor (compound 19)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: ZLM.10 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265, ZLM.10

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.230, Y.359, K.362 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.230, A:K.362 SO4.3: 6 residues within 4Å: Chain A: R.271, Y.304, T.305, I.306, R.307, Y.337 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.306, A:R.307 Water bridges: A:R.307 Salt bridges: A:R.271, A:R.307 SO4.4: 2 residues within 4Å: Chain A: K.67, K.166 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.166 Salt bridges: A:K.67, A:K.166 SO4.5: 2 residues within 4Å: Chain A: H.58, K.59 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.59 Water bridges: A:K.59 Salt bridges: A:H.58, A:K.59

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.188, A:T.191, A:V.194, H2O.3 CA.7: 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:S.198

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

PEG.8: 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 PEG.9: 4 residues within 4Å: Chain A: Y.205, F.206, P.207, G.208 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.205

1 x ZLM: (1S)-6-ethyl-N-{(1S)-1-[5-(2-ethyl-1-oxo-1,2-dihydroisoquinolin-6-yl)-1H-imidazol-2-yl]-7,7-dihydroxynonyl}-6-azaspiro[2.5]octane-1-carboxamide(Non-covalent)

ZLM.10: 20 residues within 4Å: Chain A: Q.27, G.28, H.29, P.30, M.31, E.99, D.100, H.141, H.142, G.150, F.151, D.177, H.179, F.206, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.30, A:F.151, A:F.151, A:F.151, A:F.206, A:F.206 Hydrogen bonds: A:D.100 Water bridges: A:F.206 Salt bridges: A:E.99, A:D.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, W. et al., Discovery of macrocyclic HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation. Bioorg.Med.Chem.Lett. (2021)

Release Date

2021-07-14

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 2

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