SMTL ID : 5db1.1

Menin in complex with MI-336

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x 58O: 6-methoxy-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)

58O.1: 18 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 Ligands: DMS.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.348, A:E.348 Water bridges: A:E.164, A:Y.308 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: 58O.1 No protein-ligand interaction detected (PLIP) DMS.10: 5 residues within 4Å: Chain A: V.170, G.175, E.176, Y.212, R.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214 DMS.11: 3 residues within 4Å: Chain A: F.48, F.52, P.64 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.65 pi-Cation interactions: A:F.52

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

SO4.3: 3 residues within 4Å: Chain A: Y.118, F.119, R.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.119 Salt bridges: A:R.122 SO4.4: 2 residues within 4Å: Chain A: P.17, R.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 SO4.5: 2 residues within 4Å: Chain A: K.362, R.419 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.415 Salt bridges: A:K.362, A:R.419 SO4.6: 7 residues within 4Å: Chain A: R.317, N.318, V.319, R.320, G.374, S.375, A.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.319, A:R.320, A:A.376 SO4.7: 4 residues within 4Å: Chain A: R.93, G.96, G.154, R.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.156 Salt bridges: A:R.93

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

PG4.8: 2 residues within 4Å: Chain A: Y.346, F.350 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.346, A:P.403, A:V.404 PG4.9: 4 residues within 4Å: Chain A: W.111, S.115, K.120, W.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.115 PG4.12: 7 residues within 4Å: Chain A: Y.253, D.254, G.256, E.259, L.265, K.289, S.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.254, A:G.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borkin, D. et al., Property Focused Structure-Based Optimization of Small Molecule Inhibitors of the Protein-Protein Interaction between Menin and Mixed Lineage Leukemia (MLL). J.Med.Chem. (2016)

Release Date

2016-03-30

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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