SMTL ID : 6bxy.1

Menin in complex with MI-1481

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x EEV: 4-methyl-1-{[(2S)-5-oxomorpholin-2-yl]methyl}-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1H-indole-2-carbonitrile(Non-covalent)

EEV.1: 21 residues within 4Å: Chain A: S.140, L.162, S.163, E.164, D.165, H.166, A.167, F.223, C.226, Y.261, M.263, Y.304, M.307, Y.308, G.311, W.326, E.348, E.351, V.356 Ligands: DMS.2, PG4.6 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.304, A:M.307, A:Y.308 Hydrogen bonds: A:Y.261, A:E.351 pi-Stacking: A:Y.304

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: EEV.1 No protein-ligand interaction detected (PLIP) DMS.3: 5 residues within 4Å: Chain A: F.48, F.52, G.59, P.64, V.65 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.59 pi-Cation interactions: A:F.52 DMS.4: 5 residues within 4Å: Chain A: V.407, G.408, W.409, A.410, T.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.410, A:T.411 Water bridges: A:V.407, A:W.409, A:T.411

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 3 residues within 4Å: Chain A: R.19, S.20, Y.62 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.247 PG4.6: 3 residues within 4Å: Chain A: G.311, R.315 Ligands: EEV.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.315

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 4 residues within 4Å: Chain A: Y.118, F.119, R.122, K.136 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.119 Salt bridges: A:R.122 SO4.8: 2 residues within 4Å: Chain A: K.362, R.419 5 PLIP interactions: 5 interactions with chain A Water bridges: A:Q.415, A:Q.415, A:Q.415, A:R.419 Salt bridges: A:R.419 SO4.9: 4 residues within 4Å: Chain A: R.93, G.96, G.154, R.156 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.96, A:R.156 Water bridges: A:R.93, A:G.96 Salt bridges: A:R.93

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

EDO.10: 2 residues within 4Å: Chain A: K.120, W.183 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.120, A:K.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borkin, D. et al., Complexity of Blocking Bivalent Protein-Protein Interactions: Development of a Highly Potent Inhibitor of the Menin-Mixed-Lineage Leukemia Interaction. J.Med.Chem. (2018)

Release Date

2018-11-28

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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