SMTL ID : 5mvs.1

Crystal structure of Dot1L in complex with adenosine and inhibitor CPD1 [N6-(2,6-dichlorophenyl)-N6-(pent-2-yn-1-yl)quinoline-4,6-diamine]

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

homo-dimer

Ligands

2 x ADN: ADENOSINE(Non-covalent)

ADN.1: 9 residues within 4Å: Chain A: G.164, E.187, K.188, A.189, G.222, D.223, F.224, N.242, F.246 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.188, A:K.188, A:A.189, A:D.223, A:F.224, A:N.242, A:N.242 Water bridges: A:N.242 pi-Stacking: A:F.224 ADN.4: 9 residues within 4Å: Chain B: G.164, E.187, K.188, A.189, G.222, D.223, F.224, N.242, F.246 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:K.188, B:D.223, B:F.224, B:N.242 Water bridges: B:K.188, B:K.188, B:N.242 pi-Stacking: B:F.224

2 x 5JJ: N~6~-(2,6-dichlorophenyl)-N~6~-(pent-2-yn-1-yl)quinoline-4,6-diamine(Non-covalent)

5JJ.2: 14 residues within 4Å: Chain A: F.132, T.140, S.141, L.144, V.145, F.240, V.241, N.242, V.268, S.269, S.270, V.311, S.312, Y.313 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.132, A:L.144, A:V.145, A:F.240, A:Y.313 Hydrogen bonds: A:S.141 Water bridges: A:S.141, A:S.312 pi-Stacking: A:F.240 5JJ.5: 15 residues within 4Å: Chain B: F.132, S.141, L.144, V.145, M.148, V.170, F.240, V.241, N.242, V.268, S.269, S.270, V.311, S.312, Y.313 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.132, B:L.144, B:V.145, B:V.170, B:F.240, B:N.242, B:Y.313 Hydrogen bonds: B:S.141 Water bridges: B:S.141, B:S.312 pi-Stacking: B:F.240

1 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.3: 4 residues within 4Å: Chain A: G.247, P.248, E.249, V.250 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.247, A:E.249, A:V.250

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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