SMTL ID : 5db0.1

Menin in complex with MI-352

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

PG4.1: 3 residues within 4Å: Chain A: Y.346, F.350, H.406 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.346 PG4.8: 3 residues within 4Å: Chain A: W.111, K.120, W.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.183 Water bridges: A:W.111, A:L.114 PG4.11: 5 residues within 4Å: Chain A: Y.253, D.254, L.255, G.256, E.259 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.256 Water bridges: A:E.259, A:K.289, A:K.289

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

SO4.2: 2 residues within 4Å: Chain A: P.17, R.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 SO4.3: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.317 SO4.4: 7 residues within 4Å: Chain A: R.317, N.318, V.319, R.320, G.374, S.375, A.376 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.319, A:R.320, A:A.376 Water bridges: A:R.320 Salt bridges: A:R.320 SO4.5: 2 residues within 4Å: Chain A: K.362, R.419 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.419

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

DMS.6: 3 residues within 4Å: Chain A: F.48, F.52, P.64 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.65, A:V.65 pi-Cation interactions: A:F.52 DMS.7: 6 residues within 4Å: Chain A: V.170, G.175, E.176, T.178, Y.212, R.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214 DMS.9: 7 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: 58P.10, 6E6.12, DMS.13 No protein-ligand interaction detected (PLIP) DMS.13: 7 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: DMS.9, 58P.10, 6E6.12 No protein-ligand interaction detected (PLIP)

1 x 58P: 1-[(2S)-2,3-dihydroxypropyl]-5-[(4-{[6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidin-4-yl]amino}piperidin-1-yl)methyl]-1 H-indole-2-carbonitrile(Non-covalent)

58P.10: 22 residues within 4Å: Chain A: S.140, L.162, S.163, E.164, D.165, H.166, A.167, F.223, Y.261, M.263, Y.304, M.307, Y.308, G.311, W.326, E.348, E.351, V.352, V.356 Ligands: DMS.9, 6E6.12, DMS.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.304, A:Y.304, A:M.307 Hydrogen bonds: A:Y.261, A:E.351

1 x 6E6: 1-[(2R)-2,3-dihydroxypropyl]-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)

6E6.12: 21 residues within 4Å: Chain A: S.140, L.162, S.163, E.164, D.165, H.166, A.167, F.223, Y.261, M.263, Y.304, M.307, Y.308, G.311, W.326, E.348, E.351, V.356 Ligands: DMS.9, 58P.10, DMS.13 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.304, A:Y.304, A:M.307 Hydrogen bonds: A:Y.261, A:E.351

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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