SMTL ID : 7b0t.1

Crystal structure of MLLT1 YEATS domain T3 mutant in complex with benzimidazole-amide based compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x GKT: 3-iodanyl-4-methyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide(Non-covalent)

GKT.1: 12 residues within 4Å: Chain A: F.28, H.56, S.58, F.59, P.60, E.75, S.76, G.77, Y.78, A.79, G.80, F.81 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.28, A:P.60, A:Y.78, A:A.79, A:F.81 Hydrogen bonds: A:S.58, A:S.76, A:Y.78 Water bridges: A:A.79 Salt bridges: A:E.75 pi-Stacking: A:F.28, A:H.56, A:F.59

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

EDO.2: 8 residues within 4Å: Chain A: V.9, R.10, P.39, C.42, I.44, F.47, A.136, G.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.10 EDO.3: 6 residues within 4Å: Chain A: R.16, Q.18, D.31, W.32, M.33, E.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.32 EDO.4: 4 residues within 4Å: Chain A: T.101, Y.102, D.103, R.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.103, A:R.116 EDO.5: 3 residues within 4Å: Chain A: K.111, V.112, N.113 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.113 EDO.6: 2 residues within 4Å: Chain A: E.93, E.94 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, X. et al., Structure and Inhibitor Binding Characterization of Oncogenic MLLT1 Mutants. Acs Chem.Biol. (2021)

Release Date

2021-02-17

Peptides

Protein ENL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein ENL