SMTL ID : 6x9j.1

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3830052

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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

17 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 Ligand excluded by PLIP EDO.4: 2 residues within 4Å: Chain A: R.730, Q.765 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: F.419, E.442, M.443, P.499 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: P.262, V.607, F.608, P.610, L.631, S.632, S.633 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: R.642, S.646, W.793 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: S.646, L.648, W.793, H.815, E.817, Q.818 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: W.444, N.842, D.845 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: Q.331, E.603, T.629, R.630 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: L.79, S.83, D.84, E.87, R.559, V.562, R.563 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: R.414, E.492 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: W.70, F.71, C.72, E.93 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: Y.147, S.626, I.628, T.629, L.631 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: P.499, C.500, Q.501, F.503, S.520, L.521 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Y.147, R.149, L.600, N.627 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: I.313, N.314, S.350, R.356, F.636, W.669 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: G.502, F.503, S.504, G.505, T.513, K.549 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: K.689, D.690, L.844 Chain B: A.2 Ligand excluded by PLIP

1 x X52: N-(4-{[(3,5-dicyano-4-ethyl-6-{methyl[2-(methylamino)ethyl]amino}pyridin-2-yl)sulfanyl]methyl}phenyl)-N-methylmethanesulfonamide(Non-covalent)

X52.20: 11 residues within 4Å: Chain A: C.500, Q.501, S.504, F.548, H.781, 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:K.809 Hydrogen bonds: A:S.504

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pappalardi, M.B. et al., Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Nat Cancer (2021)

Release Date

2021-07-07

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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