SMTL ID : 5dd9.1

Menin in complex with MI-326

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

1 x 59K: 4-[4-(5-methyl-1,3,4-thiadiazol-2-yl)piperazin-1-yl]-6-(2,2,2-trifluoroethyl)thieno[2,3-d]pyrimidine(Non-covalent)

59K.1: 17 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, N.267, Y.304, M.307, Y.308 Ligands: DMS.2, DMS.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.307, A:Y.308 Hydrogen bonds: A:Y.261, A:N.267 pi-Stacking: A:Y.304, A:Y.308

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

DMS.2: 6 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: 59K.1, DMS.7 No protein-ligand interaction detected (PLIP) DMS.3: 2 residues within 4Å: Chain A: F.48, F.52 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.52 DMS.7: 6 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: 59K.1, DMS.2 No protein-ligand interaction detected (PLIP) DMS.12: 2 residues within 4Å: Chain A: S.115, R.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.116 DMS.13: 5 residues within 4Å: Chain A: V.170, G.175, E.176, Y.212, R.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.214

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

PG4.4: 4 residues within 4Å: Chain A: Y.346, K.347, F.350, H.406 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.403, A:V.404 PG4.5: 6 residues within 4Å: Chain A: Y.253, D.254, G.256, E.259, L.265, K.289 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.253, A:G.256 Water bridges: A:E.259, A:E.259

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 5 residues within 4Å: Chain A: W.111, L.114, S.115, K.120, W.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.112, A:K.120

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

SO4.8: 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: 2 residues within 4Å: Chain A: P.17, R.19 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.19 SO4.10: 2 residues within 4Å: Chain A: K.362, R.419 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.415 Salt bridges: A:R.419 SO4.11: 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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