SMTL ID : 7sfc.1

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3735967A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 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

3 x I67: N-{[4-({[3,5-dicyano-4-ethyl-6-(4-methyl-1,4-diazepan-1-yl)pyridin-2-yl]sulfanyl}methyl)phenyl]methyl}glycinamide(Non-covalent)

I67.3: 12 residues within 4Å: Chain A: A.81, T.82, S.83, E.130, D.132, R.508, F.509, N.510, S.511, Y.514, M.552, R.559 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.509 Hydrogen bonds: A:S.83, A:F.509, A:R.559 Salt bridges: A:E.130 pi-Stacking: A:Y.514 I67.4: 8 residues within 4Å: Chain A: Y.49, W.70, F.71, C.72, D.76, V.91, E.95, Q.145 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.49, A:W.70, A:Q.145 Water bridges: A:E.93 pi-Stacking: A:Y.49, A:W.70 I67.25: 13 residues within 4Å: Chain A: Q.501, G.502, F.503, S.504, H.781, W.784, K.809 Chain B: C.6, G.7 Chain C: U.6, G.7, G.8 Ligands: EDO.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.784, A:K.809, A:K.809 Hydrogen bonds: A:G.502, A:S.504, A:S.504

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

EDO.5: 6 residues within 4Å: Chain A: G.579, W.669, F.670, Q.673, P.857 Ligands: EDO.13 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: L.79, S.83, D.84, E.87, R.559, V.562, R.563 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: D.84, K.111, D.133, F.138, Q.140, R.563 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: K.303, A.307, A.311 Ligand excluded by PLIP EDO.9: 7 residues within 4Å: Chain A: I.205, Y.214, G.332, R.333, N.355, R.630 Ligands: EDO.17 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: G.654, A.655, S.656, C.688, K.689, D.690, I.843 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: N.314, S.350, M.351, R.356, F.636, W.669 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: I.313, Y.578, L.605, H.606, W.669 Ligands: EDO.5, EDO.12, EDO.21 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: R.414, E.492 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: G.502, F.503, S.504, G.505, K.549 Ligands: I67.25 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: R.333, C.334, T.335, P.354, N.355 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: N.355, E.603, R.630 Ligands: EDO.9 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: W.142, D.144, R.149, E.151 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: R.484, K.488, G.489, D.490 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: M.351, Q.431, K.860 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.350, M.351, G.353, K.860, L.864 Ligands: EDO.13 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: Y.243, H.246, D.712 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: Y.147, S.626, I.628 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain A: P.374, N.375, H.376 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 10 residues within 4Å: Chain A: P.262, Q.577, P.604, H.606, V.607, F.608, P.610, C.613, L.631, S.633 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.577, A:F.608

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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