SMTL ID : 8va6.1

Menin in complex with Ziftomenib (KO-539)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

monomer

Ligands

1 x K5O: Ziftomenib(Non-covalent)

K5O.1: 27 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, D.270, Y.304, M.307, Y.308, A.310, G.311, C.314, R.315, W.326, E.348, E.351, V.352, V.356 Ligands: DMS.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.304, A:M.307, A:Y.308, A:E.351 Hydrogen bonds: A:Y.261, A:R.315, A:W.326 Water bridges: A:R.315

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.2: 5 residues within 4Å: Chain A: L.32, G.33, R.34, K.218, H.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.33 PEG.3: 8 residues within 4Å: Chain A: W.111, L.114, R.116, Y.118, K.120, W.183, K.186, G.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.120

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 SO4.7: 4 residues within 4Å: Chain A: Y.118, F.119, R.122, K.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.119 Salt bridges: A:R.122, A:K.136 SO4.9: 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

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

DMS.5: 4 residues within 4Å: Chain A: F.48, F.52, P.64, V.65 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.52 DMS.10: 6 residues within 4Å: Chain A: S.140, F.223, C.226, A.227, Y.261 Ligands: K5O.1 No protein-ligand interaction detected (PLIP)

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

PG4.6: 4 residues within 4Å: Chain A: R.57, L.60, T.61, E.240 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.240 PG4.8: 8 residues within 4Å: Chain A: Y.253, D.254, G.256, E.259, L.265, K.289, A.292, S.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.253, A:E.259, A:K.289

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

EDO.11: 4 residues within 4Å: Chain A: S.115, R.116, S.117, T.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clegg, B.D. et al., Menin in complex with Ziftomenib (KO-539). To Be Published

Release Date

2024-11-20

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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