SMTL ID : 7sff.1

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3852279B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.750, C.752, C.759, H.776 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.750, A:C.752, A:C.759, A:H.776 ZN.2: 4 residues within 4Å: Chain A: H.67, C.94, C.167, C.170 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.67, A:C.94, A:C.167, A:C.170

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

EDO.3: 5 residues within 4Å: Chain A: G.579, W.669, F.670, Q.673, P.857 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.606 EDO.4: 8 residues within 4Å: Chain A: L.79, S.83, D.84, E.87, R.559, V.562, R.563 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.83, A:D.84 EDO.5: 7 residues within 4Å: Chain A: D.84, K.111, D.133, F.138, Q.140, R.563 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.84, A:D.133, A:Q.140, A:Q.140, A:R.563 EDO.6: 3 residues within 4Å: Chain A: A.307, H.310, A.311 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.310 EDO.7: 6 residues within 4Å: Chain A: I.205, Y.214, G.332, R.333, N.355, R.630 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.333, A:N.355, A:R.630 EDO.8: 8 residues within 4Å: Chain A: G.654, A.655, S.656, I.687, C.688, K.689, D.690, I.843 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.690 EDO.9: 8 residues within 4Å: Chain A: A.118, G.489, V.491, E.492, Y.532, R.533, P.534, R.535 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.489, A:R.535 Water bridges: A:R.414

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 9 residues within 4Å: Chain A: P.262, Q.577, P.604, H.606, V.607, F.608, P.610, L.631, S.633 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.577, A:F.608

1 x C79: (2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-[4-(trifluoromethyl)phenyl]acetamide(Non-covalent)

C79.11: 9 residues within 4Å: Chain A: S.504, H.781, W.784, K.809 Chain B: C.6, G.7 Chain C: U.6, G.7, G.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.784, A:K.809

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Structural characterization of dicyanopyridine containing DNMT1-selective, non-nucleoside inhibitors. Structure (2022)

Release Date

2022-03-30

Peptides

DNA (cytosine-5)-methyltransferase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA (cytosine-5)-methyltransferase 1

Related Entries With Identical Sequence