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

Ligand binding to HDAC2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

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

PEG.1: 2 residues within 4Å: Chain A: P.340, D.341 No protein-ligand interaction detected (PLIP) PEG.2: 7 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105, G.106, E.109 Ligands: KZF.10 No protein-ligand interaction detected (PLIP) PEG.5: 7 residues within 4Å: Chain A: K.67, Y.68, L.162, L.165, A.187, F.188, T.191 No protein-ligand interaction detected (PLIP)

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.3: 6 residues within 4Å: Chain A: R.307, E.336, Y.337, F.338, G.339, P.340 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.307

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

EDO.4: 2 residues within 4Å: Chain A: N.350, M.351 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.350

1 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: KKW.9 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.7: 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.8: 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:T.191

1 x KKW: [(2~{R},4~{S})-4-(3-chlorophenyl)pyrrolidin-2-yl]-(4-thieno[2,3-c]pyridin-7-ylpiperazin-1-yl)methanone(Non-covalent)

KKW.9: 20 residues within 4Å: Chain A: Y.25, M.31, D.100, 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.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140 Water bridges: A:F.206 pi-Stacking: A:F.206, A:F.206 Halogen bonds: A:Y.25

1 x KZF: 2-(cyclohexylazaniumyl)ethanesulfonate(Non-covalent)

KZF.10: 9 residues within 4Å: Chain A: D.17, G.18, D.19, Y.23, R.56, K.59, E.109, L.113 Ligands: PEG.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.59, A:L.113 Hydrogen bonds: A:D.17, A:G.18 Salt bridges: A:R.56

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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