SMTL ID : 6t1m.1

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with benzimidazole-amide derivative 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x M8K: 4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide(Non-covalent)

M8K.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.58, A:Y.78 Water bridges: A:A.79 Salt bridges: A:E.75 pi-Stacking: A:F.28, A:H.56, A:F.59

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

EDO.2: 8 residues within 4Å: Chain A: V.9, R.10, C.42, I.44, F.47, A.138, G.139, G.140 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.10, A:G.139 EDO.3: 4 residues within 4Å: Chain A: R.16, Q.18, D.31, M.33 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.32, A:W.32 EDO.4: 3 residues within 4Å: Chain A: R.16, F.35, R.37 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.16, A:R.37 EDO.5: 2 residues within 4Å: Chain A: S.58, Y.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.78 EDO.6: 4 residues within 4Å: Chain A: K.50, R.63, V.65, K.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.50, A:R.63, A:R.63 EDO.7: 2 residues within 4Å: Chain A: D.103, F.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.103 EDO.8: 3 residues within 4Å: Chain A: F.100, T.101, R.118 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.101, A:R.118, A:R.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, X. et al., Structural Insights into Interaction Mechanisms of Alternative Piperazine-urea YEATS Domain Binders in MLLT1. Acs Med.Chem.Lett. (2019)

Release Date

2019-11-06

Peptides

Protein ENL: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein ENL

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