SMTL ID : 7sfd.1

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3543105A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 18 residues within 4Å: Chain A: F.419, S.420, G.421, C.422, G.423, G.424, L.425, E.442, M.443, W.444, E.463, D.464, C.465, G.497, L.521, N.852, A.853, V.854 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.419, A:G.421, A:C.422, A:G.423, A:G.424, A:L.425, A:M.443, A:W.444, A:D.464, A:D.464, A:C.465, A:V.854 Water bridges: A:S.426, A:N.852 pi-Stacking: A:F.419

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.3: 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

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

EDO.4: 4 residues within 4Å: Chain A: V.801, T.802 Chain C: G.7 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.802, A:T.802 Water bridges: A:N.803 EDO.5: 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.6: 2 residues within 4Å: Chain A: K.728, R.730 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.730

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: P.262, Q.577, P.604, H.606, V.607, F.608, R.630, L.631, S.632, S.633 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.577, A:H.606, A:F.608, A:R.630 GOL.8: 5 residues within 4Å: Chain A: R.584, R.586, G.851, N.852 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.584, A:R.586, A:T.800, A:N.852

1 x IO5: (2S)-2-({3,5-dicyano-4-ethyl-6-[4-(2-hydroxyethyl)-1,4-diazepan-1-yl]pyridin-2-yl}sulfanyl)-2-phenylacetamide(Non-covalent)

IO5.9: 9 residues within 4Å: Chain A: H.781, W.784, K.809 Chain B: C.6, G.7 Chain C: U.6, G.7, G.8, C.9 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

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