SMTL ID : 7b10.1

Crystal structure of MLLT1 YEATS domain T1 mutant in complex with benzimidazole-amide based compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 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: 14 residues within 4Å: Chain A: F.28, H.56, S.58, F.59, P.60, R.64, E.75, S.76, G.77, Y.78, A.79, G.80, F.81 Ligands: IOD.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.28, A:F.59, A:P.60, 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:H.56

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 3 residues within 4Å: Chain A: H.56, S.58 Ligands: GKT.1 Ligand excluded by PLIP

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

EDO.3: 9 residues within 4Å: Chain A: V.9, R.10, P.39, C.42, I.44, F.47, A.141, G.142, G.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.10, A:G.142 EDO.4: 4 residues within 4Å: Chain A: H.15, F.35, N.118, H.119 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.15 EDO.5: 6 residues within 4Å: Chain A: R.16, Q.18, D.31, W.32, M.33 Ligands: EDO.13 No protein-ligand interaction detected (PLIP) EDO.6: 6 residues within 4Å: Chain A: G.80, F.81, D.103, L.104, F.105, L.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.80, A:L.106 EDO.7: 3 residues within 4Å: Chain A: R.20, K.21, K.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.21, A:K.22, A:K.22 EDO.8: 3 residues within 4Å: Chain A: P.23, T.24, T.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.25, A:G.27 EDO.9: 3 residues within 4Å: Chain A: F.35, R.37, K.72 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.37 Water bridges: A:V.36, A:Y.71 EDO.10: 3 residues within 4Å: Chain A: Q.45, H.46, K.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.90 Water bridges: A:K.90 EDO.11: 4 residues within 4Å: Chain A: K.50, R.63, V.65, K.67 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.50, A:R.63, A:R.63, A:K.67 EDO.12: 3 residues within 4Å: Chain A: P.95, V.98, T.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.126 EDO.13: 6 residues within 4Å: Chain A: R.16, A.17, Q.18, H.116, N.118 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.118

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