SMTL ID : 7mox.1 (2 other biounits)

Structure of HDAC2 in complex with an inhibitor (compound 14)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 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: ZLS.11 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, ZLS.11

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

SO4.2: 4 residues within 4Å: Chain A: E.87, Y.88, K.90, Q.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90, A:Q.91 SO4.3: 2 residues within 4Å: Chain A: R.213, R.366 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.366 Salt bridges: A:R.213 SO4.4: 3 residues within 4Å: Chain A: S.70, D.71, K.145 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.71 Water bridges: A:S.70 Salt bridges: A:K.145 SO4.5: 3 residues within 4Å: Chain A: R.271, T.305, R.307 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.307

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 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.177, A:H.179, A:S.198, A:F.199 CA.7: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:F.188, A:V.194, H2O.3, H2O.7

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

PEG.8: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.19, A:N.22 Water bridges: A:D.105 PEG.9: 4 residues within 4Å: Chain A: R.307, E.336, Y.337, G.339 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.339 PEG.10: 5 residues within 4Å: Chain A: G.21, Y.24, H.34, R.37, Y.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.34 Water bridges: A:H.34, A:H.34

1 x ZLS: (1S)-N-[(1S)-7,7-dihydroxy-1-{4-[(1R,4S)-1,2,3,4-tetrahydro-1,4-methanonaphthalen-6-yl]-1H-imidazol-2-yl}nonyl]-6-methyl-6-azaspiro[2.5]octane-1-carboxamide(Non-covalent)

ZLS.11: 19 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, D.177, H.179, F.206, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.30, A:E.99, A:F.151, A:F.151, A:F.151, A:F.151, A:F.206, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:Y.304 Salt bridges: A:D.100 pi-Stacking: A:F.151

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
A

Histone deacetylase 2

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