SMTL ID : 4x5y.1

Menin in complex with MI-503

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

monomer

Ligands

1 x 3XW: 4-methyl-1-(1H-pyrazol-4-ylmethyl)-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)

3XW.1: 20 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, A.310, G.311, W.326, E.348, E.351, V.356 Ligands: DMS.2 6 PLIP interactions: 6 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

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: 3XW.1 No protein-ligand interaction detected (PLIP) DMS.7: 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 DMS.8: 5 residues within 4Å: Chain A: V.170, G.175, E.176, Y.212, R.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.212, A:R.214

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

PG4.3: 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

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

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: 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 SO4.6: 2 residues within 4Å: Chain A: K.362, R.419 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.362, A:R.419

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)

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 7 residues within 4Å: Chain A: N.316, R.317, N.318, V.319, R.320, G.374, A.376 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.319, A:R.320, A:A.376

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borkin, D. et al., Pharmacologic Inhibition of the Menin-MLL Interaction Blocks Progression of MLL Leukemia In Vivo. Cancer Cell (2015)

Release Date

2015-04-15

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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