SMTL ID : 9ntb.1 (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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140, A:F.206, A:L.272 Hydrogen bonds: A:H.142, A:G.150 Water bridges: A:H.179 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.3, H2O.8

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

NHE.5: 4 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.105 Hydrogen bonds: A:N.22 Water bridges: A:Y.23, A:Y.23

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

EDO.6: 4 residues within 4Å: Chain A: M.85, G.98, P.102, V.103 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.103 EDO.7: 4 residues within 4Å: Chain A: Y.16, D.17, G.18, R.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.18, A:R.56 EDO.8: 3 residues within 4Å: Chain A: R.170, Q.254, P.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.170 Water bridges: A:S.256 EDO.9: 1 residues within 4Å: Chain A: E.63 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.63 EDO.10: 5 residues within 4Å: Chain A: L.165, K.166, H.168, Q.169, R.193 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.193, A:R.193 Water bridges: A:L.165 EDO.11: 4 residues within 4Å: Chain A: N.45, Y.49, R.50 Ligands: EDO.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.50, A:R.50 EDO.12: 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:Y.49 EDO.13: 3 residues within 4Å: Chain A: N.45, Y.49 Ligands: EDO.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.49 EDO.14: 5 residues within 4Å: Chain A: R.271, Y.304, T.305, I.306, R.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.271, A:I.306, A:R.307, A:R.307 Water bridges: A:Y.304 EDO.15: 3 residues within 4Å: Chain A: N.353, Q.354, T.356 No protein-ligand interaction detected (PLIP) EDO.20: 4 residues within 4Å: Chain A: N.126, R.127, Q.128, Y.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.126

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

PEG.16: 3 residues within 4Å: Chain A: E.53, I.54, Y.55 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.53 PEG.17: 4 residues within 4Å: Chain A: Q.128, Q.129, T.130, D.131 No protein-ligand interaction detected (PLIP) PEG.18: 3 residues within 4Å: Chain A: E.336, Y.337, G.339 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.307 PEG.19: 1 residues within 4Å: Chain A: H.34 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.22, A:R.37 Water bridges: A:Y.337, A:Y.337

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

PGE.21: 7 residues within 4Å: Chain A: Q.169, R.170, D.192, Y.223, M.252, Y.253, Q.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.169

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
A

Histone deacetylase 2

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