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

Ligand binding to HDAC2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 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: KJF.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, 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.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:Y.223

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

PEG.4: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.19, A:N.22 PEG.5: 6 residues within 4Å: Chain A: G.21, N.22, Y.24, H.34, R.37, Y.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.22, A:R.37, A:Y.337, A:Y.337

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

PGE.6: 1 residues within 4Å: Chain A: R.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.127

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

KJF.7: 21 residues within 4Å: Chain A: Y.25, M.31, R.35, F.110, G.138, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140, A:F.151, A:F.151, A:F.206 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

Related Entries With Identical Sequence