SMTL ID : 9ntb.2 (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: 23 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, PEG.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140, A:L.140, A:F.206, A:L.272 Hydrogen bonds: A:D.100, A:H.142, A:G.150 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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, 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.175, A:D.177, A:H.179, A:S.198 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.4, H2O.6

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.5: 8 residues within 4Å: Chain A: D.17, G.18, D.19, R.56, K.59, E.109, L.113 Ligands: EDO.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:K.59, A:E.109, A:L.113 Hydrogen bonds: A:D.17 Salt bridges: A:R.56

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

PEG.6: 5 residues within 4Å: Chain A: Y.49, R.50, K.51, M.52, E.53 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.53 PEG.11: 6 residues within 4Å: Chain A: Q.27, G.28, H.29, P.30, D.100 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.27 PEG.14: 5 residues within 4Å: Chain A: R.307, E.336, Y.337, G.339, P.340 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.307 PEG.15: 1 residues within 4Å: Chain A: A.187 No protein-ligand interaction detected (PLIP) PEG.16: 5 residues within 4Å: Chain A: R.170, D.192, Y.223, M.252, Y.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192

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

EDO.7: 3 residues within 4Å: Chain A: Y.167, H.168, S.256 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.167 Water bridges: A:Q.128, A:S.256 EDO.8: 2 residues within 4Å: Chain A: P.348 Ligands: PG4.17 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.235, A:D.235, A:D.235, A:I.346, A:S.347 EDO.9: 2 residues within 4Å: Chain A: L.44, N.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.45 EDO.10: 2 residues within 4Å: Chain A: N.350, T.352 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.350, A:T.352 Water bridges: A:N.350 EDO.12: 5 residues within 4Å: Chain A: Y.16, D.17, G.18, R.56 Ligands: NHE.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.18, A:R.56 Water bridges: A:H.40 EDO.13: 5 residues within 4Å: Chain A: K.10, D.131, N.293, L.294, P.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.131 Water bridges: A:K.10, A:K.10

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

PG4.17: 6 residues within 4Å: Chain A: K.280, Y.315, E.324, N.327, H.345 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.280 PG4.18: 5 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105, E.109 No protein-ligand interaction detected (PLIP)

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
B

Histone deacetylase 2

Related Entries With Identical Sequence