SMTL ID : 6by8.1

Menin in complex with MI-1482

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x FNV: 4-methyl-1-{[(2R)-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)

FNV.1: 20 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, W.326, E.348, E.351, V.356 Ligands: DMS.2, PG4.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.304, A:M.307, A:Y.308 Hydrogen bonds: A:E.351 Water bridges: A:E.164, A:Y.308, A:E.351, A:E.351

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

DMS.2: 5 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: FNV.1 No protein-ligand interaction detected (PLIP) DMS.3: 6 residues within 4Å: Chain A: V.170, G.175, E.176, T.178, Y.212, R.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.212, A:R.214 DMS.4: 2 residues within 4Å: Chain A: F.48, F.52 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.52 DMS.5: 4 residues within 4Å: Chain A: N.267, D.270, L.271, L.274 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.267

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

PG4.6: 3 residues within 4Å: Chain A: C.314, R.315 Ligands: FNV.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.315 PG4.10: 2 residues within 4Å: Chain A: L.60, T.61 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.57, A:R.57

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

SO4.7: 2 residues within 4Å: Chain A: K.362, R.419 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.415 Salt bridges: A:R.419 SO4.8: 3 residues within 4Å: Chain A: Y.118, F.119, K.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.119

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

EDO.9: 3 residues within 4Å: Chain A: W.111, K.120, W.183 No protein-ligand interaction detected (PLIP)

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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