SMTL ID : 9jv3.1 (2 other biounits)

Structure of Human HDAC2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 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, G.302 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265

2 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 CA.3: 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.2, H2O.3

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

EDO.4: 5 residues within 4Å: Chain A: K.166, Y.167, H.168, Q.169, R.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.167, A:Q.169 EDO.8: 4 residues within 4Å: Chain A: Y.46, G.47, R.50, C.323 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.46 EDO.9: 3 residues within 4Å: Chain A: L.44, N.45, R.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.50 EDO.10: 2 residues within 4Å: Chain A: G.21, H.34 No protein-ligand interaction detected (PLIP)

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

PEG.5: 5 residues within 4Å: Chain A: R.170, D.192, Y.223, M.252, Y.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.169, A:M.252 PEG.7: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.19, A:N.22

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

PGE.6: 6 residues within 4Å: Chain A: L.162, L.165, A.187, F.188, T.191, R.193 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tojo, T. et al., Discovery of an HDAC2-selective inhibitor based on enzyme-inhibitor binding thermodynamics and kinetics, and its potential as a therapeutic drug for neurological disorders. To Be Published

Release Date

2025-10-08

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone deacetylase 2

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