SMTL ID : 7zzu.3 (2 other biounits)

Inhibitory Ligand binding to HDAC2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

PEG.1: 7 residues within 4Å: Chain A: Y.68, L.162, L.165, A.187, F.188, T.191, R.193 No protein-ligand interaction detected (PLIP)

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

EDO.2: 8 residues within 4Å: Chain A: K.10, D.131, M.132, K.290, N.293, L.294, P.295, L.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.290 Water bridges: A:L.294

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: KKI.6 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.4: 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.5: 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:F.188

1 x KKI: 2-[4-[(2~{R},4~{S})-4-phenylpyrrolidin-2-yl]carbonylpiperazin-1-yl]pyridine-3-carbonitrile(Non-covalent)

KKI.6: 19 residues within 4Å: Chain A: M.31, R.35, D.100, 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.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.140, A:F.206 Hydrogen bonds: A:G.150, A:Y.304 Water bridges: A:F.206

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
C

Histone deacetylase 2

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