SMTL ID : 9ntb.3 (2 other biounits)

Crystal structure of human HDAC2 in complex with TNG260

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x 01: (R)-N-(4-amino-4'-fluoro-[1,1'-biphenyl]-3-yl)-4-(S-methylsulfonimidoyl)benzamide

01.1: 22 residues within 4Å: Chain A: Y.25, M.31, R.35, D.100, F.110, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, Q.261, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140, A:L.140, A:F.206, A:L.272 Hydrogen bonds: A:H.142, A:G.150, A:Y.304 Water bridges: A:H.179, A:L.272 pi-Stacking: A:F.151

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: 01.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.177, A:H.179, A:D.265

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.177, A:H.179, A:S.198, A:F.199 CA.4: 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:F.188, A:T.191, A:V.194, H2O.3, H2O.5

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

EDO.5: 4 residues within 4Å: Chain A: M.92, N.96, V.97, E.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.96 EDO.6: 5 residues within 4Å: Chain A: K.166, Y.167, H.168, Q.169, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.167 EDO.7: 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:K.290 Water bridges: A:L.294 EDO.8: 1 residues within 4Å: Chain A: I.54 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.54 EDO.9: 5 residues within 4Å: Chain A: Q.169, R.170, D.192, R.193, Y.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.169, A:Y.223 Water bridges: A:Y.223

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

PGE.10: 6 residues within 4Å: Chain A: L.162, L.165, A.187, F.188, T.191, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.193

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahronian, L.G. et al., TNG260 is a Small-Molecule CoREST Inhibitor that Sensitizes STK11-Mutant Tumors to Anti-PD-1 Immunotherapy. Cancer Res. (2025)

Release Date

2025-09-17

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Histone deacetylase 2

Related Entries With Identical Sequence