SMTL ID : 5mw4.2 (1 other biounit)

Crystal structure of Dot1L in complex with inhibitor CPD7 [N-(3-(((R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl)(methyl)amino)propyl)-2-(3-(2-chloro-3-(2-methylpyridin-3-yl)benzo[b]thiophen-5-yl)ureido)acetamide]

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

1 x 5JU: N~2~-{[2-chloro-3-(2-methylpyridin-3-yl)-1-benzothiophen-5-yl]carbamoyl}-N-(3-{methyl[(3R)-1-(5H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]amino}propyl)glycinamide(Non-covalent)

5JU.1: 23 residues within 4Å: Chain A: S.141, L.144, V.145, M.148, D.162, G.164, S.165, G.166, V.170, E.187, K.188, G.222, D.223, F.224, F.240, V.241, N.242, F.246, V.268, S.269, S.270, S.312, Y.313 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.144, A:V.145, A:K.188, A:F.240, A:N.242 Hydrogen bonds: A:D.162, A:D.162, A:G.164, A:K.188, A:F.224, A:N.242 Water bridges: A:G.168, A:N.242 Salt bridges: A:E.187 pi-Stacking: A:F.224, A:F.224 pi-Cation interactions: A:K.188 Halogen bonds: A:S.312

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

SO4.2: 4 residues within 4Å: Chain A: R.9, K.11, N.80, R.81 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.77, A:N.80 Water bridges: A:K.11 Salt bridges: A:R.9, A:R.81 SO4.3: 3 residues within 4Å: Chain A: T.101, R.102, K.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.100, A:R.102 Water bridges: A:K.213 Salt bridges: A:R.102, A:K.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mobitz, H. et al., Discovery of Potent, Selective, and Structurally Novel Dot1L Inhibitors by a Fragment Linking Approach. ACS Med Chem Lett (2017)

Release Date

2017-03-22

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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