SMTL ID : 7moz.2 (2 other biounits)

Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 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: ZL4.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.177, A:H.179, A:D.265, ZL4.8

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

SO4.2: 4 residues within 4Å: Chain A: E.87, Y.88, K.90, Q.91 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.90, A:Q.91, A:Q.91 Water bridges: A:R.94 Salt bridges: A:K.90 SO4.3: 2 residues within 4Å: Chain A: T.305, R.307 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.307 Salt bridges: A:R.307

2 x CA: CALCIUM ION(Non-covalent)

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.177, A:H.179, A:S.198, A:F.199 CA.5: 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.5, H2O.10

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

PEG.6: 2 residues within 4Å: Chain A: N.350, T.352 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.350 Water bridges: A:T.352 PEG.7: 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.105 Water bridges: A:D.19, A:N.22

1 x ZL4: (1R,3S,6S,18R,27R)-6-(6,6-dihydroxyoctyl)-5,8,18,27,34-pentaazahexacyclo[25.2.2.1~7,10~.1~11,15~.1~14,18~.0~1,3~]tetratriaconta-7,9,11(33),12,14,16-hexaene-4,32-dione (non-preferred name)(Non-covalent)

ZL4.8: 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 13 PLIP interactions: 13 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:Y.304 Water bridges: A:F.206, A:R.271 Salt bridges: A:E.99, A:D.100 pi-Stacking: A:P.30, A:P.30

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
B

Histone deacetylase 2

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