SMTL ID : 8va5.1

Menin mutant - T349M in complex with Ziftomenib (KO-539)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 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.7 12 PLIP interactions: 12 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:R.315, A:W.326 Water bridges: A:E.164, A:R.315 Salt bridges: A:E.351 pi-Stacking: A:Y.304

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

PEG.2: 7 residues within 4Å: Chain A: W.111, L.114, S.115, R.116, Y.118, K.120, W.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.111, A:K.120 Water bridges: A:L.114 PEG.4: 2 residues within 4Å: Chain A: T.61, Y.62 No protein-ligand interaction detected (PLIP)

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

PG4.3: 4 residues within 4Å: Chain A: Y.346, K.347, F.350, H.406 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.406 Water bridges: A:Y.338

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

EDO.5: 6 residues within 4Å: Chain A: V.170, G.175, E.176, T.178, Y.212, R.214 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.212, A:R.214, A:R.214

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

DMS.6: 5 residues within 4Å: Chain A: F.48, F.52, V.58, P.64, V.65 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: S.140, F.223, C.226, A.227, Y.261 Ligands: K5O.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, E.S. et al., Ziftomenib in relapsed or refractory acute myeloid leukaemia (KOMET-001): a multicentre, open-label, multi-cohort, phase 1 trial. Lancet Oncol (2024)

Release Date

2024-11-20

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin