SMTL ID : 5ddb.1

Menin in complex with MI-319

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

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

59Q.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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.261, A:N.267 pi-Stacking: A:Y.304, A:Y.308 Halogen bonds: A:Y.304

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: 59Q.1, DMS.7 No protein-ligand interaction detected (PLIP) DMS.3: 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.7: 6 residues within 4Å: Chain A: S.140, F.223, C.226, A.227 Ligands: 59Q.1, DMS.2 No protein-ligand interaction detected (PLIP) DMS.11: 2 residues within 4Å: Chain A: K.104, R.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.192 Salt bridges: A:D.108 DMS.12: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.346 PG4.5: 4 residues within 4Å: Chain A: E.259, K.289, A.292, S.293 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.259 Water bridges: A:E.259

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

PEG.6: 4 residues within 4Å: Chain A: W.111, S.115, K.120, W.183 No protein-ligand interaction detected (PLIP)

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

SO4.8: 3 residues within 4Å: Chain A: 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 SO4.9: 4 residues within 4Å: Chain A: R.93, G.96, G.154, R.156 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.96, A:R.156 Salt bridges: A:R.93, A:R.156 SO4.10: 2 residues within 4Å: Chain A: K.362, R.419 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.415 Salt bridges: A:K.362, A:R.419 SO4.13: 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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