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

HDAC2 in complex with an inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: KIZ.4 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.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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.223 Water bridges: A:T.196

1 x KIZ: [(2~{R})-1-(dimethylamino)-3-(4-fluorophenyl)-1-oxidanylidene-propan-2-yl]azanium(Non-covalent)

KIZ.4: 18 residues within 4Å: Chain A: M.31, R.35, 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 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.140, A:F.151 Hydrogen bonds: A:H.141, A:G.302, A:Y.304 Halogen bonds: A:R.35

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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