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

HDAC2 in complex with inhibitory ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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: KJN.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.177, A:H.179, A:D.265

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 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

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.188

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: L.165, K.166, Y.167, H.168, Q.169, R.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.165, A:R.193 Water bridges: A:Q.169 EDO.5: 4 residues within 4Å: Chain A: R.307, E.336, Y.337, G.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.339 Water bridges: A:R.307, A:G.339 EDO.6: 4 residues within 4Å: Chain A: Y.68, L.162, A.187, F.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.145, A:K.145 EDO.7: 7 residues within 4Å: Chain A: I.215, Y.222, A.224, V.225, N.370, L.371, L.374 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.215 Water bridges: A:N.370

1 x KJN: [(2~{R})-1-(dimethylamino)-1-oxidanylidene-4-phenyl-butan-2-yl]azanium(Non-covalent)

KJN.8: 20 residues within 4Å: Chain A: Y.25, M.31, R.35, F.110, G.139, L.140, 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.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.140, A:F.151 Hydrogen bonds: A:H.141, A:G.302, A:Y.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamanini, E. et al., Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. Acs Med.Chem.Lett. (2022)

Release Date

2022-09-21

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 2

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