SMTL ID : 6t1l.1

Crystal structure of MLLT1 (ENL) YEATS domain in complexed with piperazine-urea derivative 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

EDO.1: 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 EDO.2: 3 residues within 4Å: Chain A: E.94, R.96, K.97 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.96, A:K.97 EDO.3: 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.4: 5 residues within 4Å: Chain A: R.16, Q.18, D.31, W.32, M.33 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.32 EDO.5: 2 residues within 4Å: Chain A: F.35, R.37 No protein-ligand interaction detected (PLIP) EDO.6: 4 residues within 4Å: Chain A: D.43, Q.45, H.46, K.90 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.46, A:K.90 Water bridges: A:Q.45, A:Q.45 EDO.7: 4 residues within 4Å: Chain A: P.95, L.122, T.123, F.124 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.123, A:T.123 EDO.8: 2 residues within 4Å: Chain A: D.103, F.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.103 EDO.9: 4 residues within 4Å: Chain A: L.136, G.140, V.141, M.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.142 EDO.10: 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

1 x M7N: ~{N}-[[4-(diethylaminomethyl)phenyl]methyl]-4-pyrimidin-2-yl-piperazine-1-carboxamide(Non-covalent)

M7N.11: 11 residues within 4Å: Chain A: F.28, H.56, S.58, F.59, P.60, S.76, G.77, Y.78, A.79, G.80, F.81 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.78, A:A.79, A:F.81 Hydrogen bonds: A:S.58, A:S.58, A:Y.78, A:A.79 pi-Stacking: A:H.56

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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