SMTL ID : 7uj4.1

Inhibition of Human Menin by SNDX-5613

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

2 x OQ4: 2-({4-[7-({(1r,4r)-4-[(ethanesulfonyl)amino]cyclohexyl}methyl)-2,7-diazaspiro[3.5]nonan-2-yl]pyrimidin-5-yl}oxy)-N-ethyl-5-fluoro-N-(propan-2-yl)benzamide(Non-covalent)

OQ4.1: 20 residues within 4Å: Chain A: S.155, S.178, E.179, D.180, H.181, A.182, F.238, C.241, A.242, Y.276, M.278, Y.319, M.322, Y.323, G.326, W.341, E.363, E.366, V.367 Ligands: MG.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.238, A:F.238, A:A.242, A:Y.319, A:M.322 Hydrogen bonds: A:G.326 OQ4.4: 21 residues within 4Å: Chain B: S.155, L.177, S.178, E.179, D.180, H.181, A.182, F.238, C.241, A.242, Y.276, M.278, Y.319, M.322, Y.323, A.325, G.326, W.341, E.363, E.366, V.367 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.238, B:Y.319, B:M.322, B:V.367

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.180, E.359 Ligands: OQ4.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.180, A:E.359, H2O.1, H2O.1, H2O.3 MG.3: 1 residues within 4Å: Chain A: D.350 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.350, H2O.1, H2O.1, H2O.4, H2O.4 MG.5: 2 residues within 4Å: Chain B: D.180, E.359 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.180, B:E.359, H2O.5, H2O.6, H2O.6, H2O.7 MG.6: 2 residues within 4Å: Chain B: E.316, D.350 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.350, H2O.5, H2O.5, H2O.6, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Perner, F. et al., MEN1 mutations mediate clinical resistance to menin inhibition. Nature (2023)

Release Date

2022-12-14

Peptides

Isoform 2 of Menin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Isoform 2 of Menin