SMTL ID : 8ig0.1 (1 other biounit)

Crystal structure of menin in complex with DS-1594b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x 7IX: (1R,2S,4R)-4-[[4-(5,6-dimethoxypyridazin-3-yl)phenyl]methylamino]-2-[methyl-[6-[2,2,2-tris(fluoranyl)ethyl]thieno[2,3-d]pyrimidin-4-yl]amino]cyclopentan-1-ol(Non-covalent)

7IX.1: 22 residues within 4Å: Chain A: S.155, L.177, S.178, E.179, D.180, H.181, A.182, F.238, C.241, Y.276, M.278, Y.319, M.322, Y.323, G.326, C.329, W.341, E.363, E.366, V.367, V.371 Ligands: DMS.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.319, A:Y.319, A:M.322, A:E.363 Hydrogen bonds: A:E.363 Water bridges: A:N.282 pi-Stacking: A:W.341 7IX.4: 21 residues within 4Å: Chain B: S.155, L.177, E.179, D.180, H.181, A.182, F.238, C.241, Y.276, M.278, Y.319, M.322, Y.323, G.326, C.329, W.341, E.363, E.366, V.367, V.371 Ligands: DMS.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.319, B:M.322, B:E.363 pi-Stacking: B:W.341

2 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.2: 6 residues within 4Å: Chain A: Q.349, Y.351, N.352, K.422, W.423, E.425 No protein-ligand interaction detected (PLIP) UNX.5: 6 residues within 4Å: Chain B: Q.349, Y.351, N.352, K.422, W.423, E.425 No protein-ligand interaction detected (PLIP)

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

DMS.3: 2 residues within 4Å: Chain A: C.241 Ligands: 7IX.1 No protein-ligand interaction detected (PLIP) DMS.6: 2 residues within 4Å: Chain B: A.242 Ligands: 7IX.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Numata, M. et al., A novel Menin-MLL1 inhibitor, DS-1594a, prevents the progression of acute leukemia with rearranged MLL1 or mutated NPM1. Cancer Cell Int (2023)

Release Date

2023-03-22

Peptides

Menin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Menin

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