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

Structure of HDAC2 complexed with an inhibitory ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 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: 2OP.12 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, 2OP.12

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.175, A:D.177, A:H.179, A:S.198

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:T.191

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22

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

EDO.5: 4 residues within 4Å: Chain A: N.41, L.44, N.45, Y.49 No protein-ligand interaction detected (PLIP) EDO.6: 5 residues within 4Å: Chain A: G.21, N.22, Y.24, H.34, R.37 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.37 EDO.7: 5 residues within 4Å: Chain A: K.11, Q.128, Q.129, T.130, D.131 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.129 Water bridges: A:D.131, A:D.131 EDO.8: 4 residues within 4Å: Chain A: Y.68, L.162, A.187, F.188 No protein-ligand interaction detected (PLIP) EDO.9: 3 residues within 4Å: Chain A: N.353, Q.354, T.356 No protein-ligand interaction detected (PLIP) EDO.10: 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 Water bridges: A:Q.169, A:R.193

1 x KJ6: 6-methyl-4-oxidanyl-pyran-2-one(Non-covalent)

KJ6.11: 8 residues within 4Å: Chain A: D.100, H.142, G.150, F.151, H.179, F.206, Y.304 Ligands: 2OP.12 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.151, A:F.151 Hydrogen bonds: A:D.100 Water bridges: A:G.150, A:Y.205 Salt bridges: A:H.179 pi-Stacking: A:F.206

1 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.12: 16 residues within 4Å: Chain A: M.31, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, D.265, G.301, G.302, Y.304 Ligands: ZN.1, KJ6.11 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.302, A:Y.304, A:Y.304, A:Y.304 Salt bridges: A:H.141, A:H.142, A:H.179

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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