SMTL ID : 9hgm.1

Structure of human DNMT2 with bound allosteric inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x 01: 4-ethyl-~{N}-[[1-[[(2~{R})-1-(1~{H}-indol-3-yl)-4-[[2-(methylamino)-2-oxidanylidene-ethyl]amino]-4-oxidanylidene-butan-2-yl]carbamoyl]cyclopropyl]methyl]benzamide

01.1: 25 residues within 4Å: Chain A: Y.12, M.77, S.78, P.79, P.80, Q.82, R.97, T.98, F.101, L.120, E.121, N.122, V.123, G.125, F.126, S.129, T.131, L.135, N.332 Chain B: L.235, L.236, L.237, D.238, E.259 Ligands: GOL.4 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.12, A:R.97, A:F.101, A:F.101, A:L.120, A:L.120, A:N.122, A:F.126, A:L.135, B:L.235, B:L.236, B:D.238 Hydrogen bonds: A:Q.82, A:E.121, A:N.122, A:N.122, A:N.332, B:L.235 pi-Stacking: A:F.126 01.3: 26 residues within 4Å: Chain A: L.235, L.236, L.237, D.238, E.259 Chain B: Y.12, M.77, S.78, P.79, P.80, Q.82, R.97, T.98, F.101, L.120, E.121, N.122, V.123, G.125, F.126, S.129, T.131, L.135, Y.165, N.332 Ligands: GOL.2 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.12, B:F.101, B:F.101, B:L.120, B:L.120, B:N.122, B:F.126, B:L.135, A:L.235, A:L.236, A:D.238 Hydrogen bonds: B:R.97, B:E.121, B:N.122, B:N.122, B:T.131, B:N.332, A:E.259 pi-Stacking: B:F.126

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: L.236, L.237, D.238, V.248, I.258, E.259, G.260, T.261, G.262, S.263 Ligands: 01.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.236, A:D.238, A:G.260, A:G.260 GOL.4: 10 residues within 4Å: Chain B: L.236, L.237, D.238, V.248, I.258, E.259, G.260, T.261, G.262 Ligands: 01.1 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.236, B:D.238, B:G.260, B:G.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frey, A.F. et al., DNA-encoded library screening uncovers potent DNMT2 inhibitors targeting a cryptic allosteric binding site. Iscience (2025)

Release Date

2025-08-27

Peptides

tRNA (cytosine(38)-C(5))-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (cytosine(38)-C(5))-methyltransferase