SMTL ID : 3sx0.1

Crystal structure of Dot1l in complex with a brominated SAH analog

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

monomer

Ligands

1 x SX0: (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(4-amino-5-bromo-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)(Non-covalent)

SX0.1: 21 residues within 4Å: Chain A: P.134, V.136, Y.137, G.138, E.139, T.140, D.162, G.164, S.165, Q.169, V.170, E.187, K.188, G.222, D.223, F.224, F.240, N.242, F.246, V.250 Ligands: UNX.19 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.140, A:T.140, A:G.164, A:Q.169, A:K.188, A:D.223, A:D.223, A:F.224, A:N.242 Water bridges: A:E.135 pi-Stacking: A:F.224

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: R.204, K.208, H.214 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.204, A:K.208, A:H.214

20 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.3: 4 residues within 4Å: Chain A: A.19, K.205, W.206, W.209 Ligand excluded by PLIP UNX.4: 1 residues within 4Å: Chain A: H.110 Ligand excluded by PLIP UNX.5: 1 residues within 4Å: Chain A: R.102 Ligand excluded by PLIP UNX.6: 1 residues within 4Å: Chain A: T.105 Ligand excluded by PLIP UNX.7: 1 residues within 4Å: Ligands: UNX.8 Ligand excluded by PLIP UNX.8: 1 residues within 4Å: Ligands: UNX.7 Ligand excluded by PLIP UNX.9: 3 residues within 4Å: Chain A: S.104, L.107, K.212 Ligand excluded by PLIP UNX.10: 5 residues within 4Å: Chain A: R.109, S.141, F.142, D.143 Ligands: UNX.11 Ligand excluded by PLIP UNX.11: 3 residues within 4Å: Chain A: S.141, F.142 Ligands: UNX.10 Ligand excluded by PLIP UNX.12: 3 residues within 4Å: Chain A: Y.184, R.232, T.236 Ligand excluded by PLIP UNX.13: 3 residues within 4Å: Chain A: R.204, E.216, Y.217 Ligand excluded by PLIP UNX.14: 2 residues within 4Å: Chain A: S.226, E.227 Ligand excluded by PLIP UNX.15: 3 residues within 4Å: Chain A: R.230, Q.253, R.257 Ligand excluded by PLIP UNX.16: 2 residues within 4Å: Chain A: H.252, K.255 Ligand excluded by PLIP UNX.17: 2 residues within 4Å: Chain A: N.281, S.282 Ligand excluded by PLIP UNX.18: 2 residues within 4Å: Chain A: Q.147, D.150 Ligand excluded by PLIP UNX.19: 3 residues within 4Å: Chain A: K.188, L.225 Ligands: SX0.1 Ligand excluded by PLIP UNX.20: 2 residues within 4Å: Chain A: A.189, D.190 Ligand excluded by PLIP UNX.21: 2 residues within 4Å: Chain A: H.118, E.202 Ligand excluded by PLIP UNX.22: 1 residues within 4Å: Chain A: S.328 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, W. et al., Bromo-deaza-SAH: a potent and selective DOT1L inhibitor. Bioorg. Med. Chem. (2013)

Release Date

2011-07-27

Peptides

Histone-lysine N-methyltransferase, H3 lysine-79 specific: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase, H3 lysine-79 specific

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