SMTL ID : 5dde.1

Menin in complex with MI-859

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

2 x 5A0: 6-(2,2-difluoroethyl)-4-[4-(5,5-dimethyl-4,5-dihydro-1,3-thiazol-2-yl)piperazin-1-yl]thieno[2,3-d]pyrimidine(Non-covalent)

5A0.1: 17 residues within 4Å: Chain A: S.140, L.162, S.163, D.165, H.166, A.167, F.223, C.226, Y.261, M.263, N.267, Y.304, M.307, Y.308 Ligands: 5A0.2, DMS.7, DMS.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.307, A:Y.308 Hydrogen bonds: A:Y.261, A:N.267 5A0.2: 16 residues within 4Å: Chain A: S.140, L.162, S.163, H.166, A.167, F.223, C.226, Y.261, M.263, N.267, Y.304, M.307, Y.308 Ligands: 5A0.1, DMS.7, DMS.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:M.307, A:Y.308 Hydrogen bonds: A:Y.261, A:N.267

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

SO4.3: 0 residues within 4Å: (No contacts) 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.56 SO4.4: 2 residues within 4Å: Chain A: P.17, R.19 2 PLIP interactions: 2 interactions with chain A Water bridges: A:F.16 Salt bridges: A:R.19 SO4.5: 2 residues within 4Å: Chain A: K.362, R.419 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.415, A:R.419 Salt bridges: A:R.419 SO4.6: 4 residues within 4Å: Chain A: S.117, Y.118, F.119, R.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.119 Salt bridges: A:R.122, A:K.136

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

DMS.7: 7 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: 5A0.1, 5A0.2, DMS.8 No protein-ligand interaction detected (PLIP) DMS.8: 7 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: 5A0.1, 5A0.2, DMS.7 No protein-ligand interaction detected (PLIP) DMS.9: 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.11: 5 residues within 4Å: Chain A: V.170, G.175, E.176, Y.212, R.214 No protein-ligand interaction detected (PLIP)

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

PG4.10: 4 residues within 4Å: Chain A: Y.346, K.347, F.350, H.406 No protein-ligand interaction detected (PLIP)

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

EDO.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pollock, J. et al., Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J.Med.Chem. (2015)

Release Date

2015-09-09

Peptides

Menin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Menin

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