SMTL ID : 6o5i.1

Menin in complex with MI-3454

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

monomer

Ligands

1 x LMY: ~{N}-[3-[[2-cyano-4-methyl-5-[[4-[[2-(methylamino)-6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]piperidin-1-yl]methyl]indol-1-yl]methyl]-1-bicyclo[1.1.1]pentanyl]methanamide(Non-covalent)

LMY.1: 23 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, A.264, N.267, Y.304, M.307, Y.308, A.310, G.311, W.326, E.348, E.351, V.356 Ligands: DMS.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.304, A:M.307, A:Y.308, A:E.351, A:V.356 Hydrogen bonds: A:Y.261, A:Y.261, A:Y.308, 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: LMY.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.140 DMS.3: 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.4: 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.5: 1 residues within 4Å: Chain A: Y.62 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.243, A:Q.243

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

SO4.6: 2 residues within 4Å: Chain A: P.17, R.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 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: 7 residues within 4Å: Chain A: R.317, N.318, V.319, R.320, G.374, S.375, A.376 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.319, A:R.320, A:A.376 Water bridges: A:R.317, A:R.320, A:R.320 Salt bridges: A:R.320

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

PG4.9: 3 residues within 4Å: Chain A: Y.346, F.350, H.406 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Klossowski, S. et al., Menin inhibitor MI-3454 induces remission in MLL1-rearranged and NPM1-mutated models of leukemia. J.Clin.Invest. (2020)

Release Date

2020-01-08

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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