SMTL ID : 9jv3.3 (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: 3 residues within 4Å: Chain A: D.177, H.179, D.265 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: 7 residues within 4Å: Chain A: D.175, I.176, 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:H.179, A:S.198, A:F.199 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:T.191, A:V.194, A:Y.223, H2O.2, H2O.2

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

PEG.4: 3 residues within 4Å: Chain A: A.187, F.188, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.193 PEG.9: 3 residues within 4Å: Chain A: D.19, N.22, Y.23 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.22

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

EDO.5: 4 residues within 4Å: Chain A: K.166, Y.167, Q.169, R.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.165, A:R.193 EDO.6: 3 residues within 4Å: Chain A: R.170, Y.253 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.223, A:Y.223 EDO.7: 4 residues within 4Å: Chain A: R.170, D.192, Y.223 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.170, A:Y.223, A:Y.223 EDO.8: 5 residues within 4Å: Chain A: K.10, D.131, K.290, N.293, L.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.10, A:N.293 Water bridges: A:D.131

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
C

Histone deacetylase 2

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