SMTL ID : 6x9i.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

SAH.1: 19 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, P.499, L.521, N.852, A.853, V.854 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:F.419, A:C.422, A:G.423, A:G.424, A:L.425, A:M.443, A:W.444, A:D.464, A:C.465, A:G.497, A:V.854 Water bridges: A:S.426, A:N.852, 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

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

EDO.4: 5 residues within 4Å: Chain A: S.547, R.550, S.551, V.618 Chain B: G.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.547, A:S.551, A:V.618 Water bridges: A:R.550 EDO.6: 4 residues within 4Å: Chain A: P.456, G.457, S.458, T.459 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.457, A:S.458, A:T.459, A:V.460 EDO.7: 6 residues within 4Å: Chain A: S.646, L.648, W.793, H.815, E.817, Q.818 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.648, A:E.817, A:E.817, A:Q.818 EDO.8: 3 residues within 4Å: Chain A: F.840, G.841, K.846 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.841, A:K.846, A:K.846

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.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

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

Related Entries With Identical Sequence