SMTL ID : 8eye.1

Plasmodium falciparum M1 in complex with inhibitor 9aj

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: V.300, H.303, E.304, E.333, Y.387 Ligands: X4I.6, GOL.11 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.304, A:E.304, A:E.333 Water bridges: A:R.296 GOL.2: 8 residues within 4Å: Chain A: V.266, G.267, N.278, N.280, S.281, R.296, N.801, R.804 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.278, A:N.280, A:N.280, A:S.281, A:S.281, A:R.296, A:R.804 Water bridges: A:Q.845 GOL.4: 10 residues within 4Å: Chain A: K.286, Y.687, F.688, H.693, V.694, D.695, Q.698, M.699, R.702, Y.732 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.286, A:Y.687, A:D.695, A:D.695, A:R.702, A:R.702, A:Y.732 Water bridges: A:Y.732 GOL.8: 5 residues within 4Å: Chain A: A.110, T.112, R.132, E.379, P.840 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.112, A:T.112, A:R.132 Water bridges: A:M.841, A:N.880 GOL.9: 8 residues within 4Å: Chain A: Y.572, C.575, T.576, Y.579, Y.630, S.633, L.634, P.635 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.572 GOL.11: 6 residues within 4Å: Chain A: V.330, E.333, N.334, H.350, D.388 Ligands: GOL.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.333, A:D.388 Water bridges: A:R.296, A:T.299, A:T.384

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

DMS.3: 4 residues within 4Å: Chain A: N.380, Y.382, T.844, Y.884 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.382, A:Y.884 DMS.5: 5 residues within 4Å: Chain A: P.505, E.506, N.507, G.508, Y.564 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.564 DMS.7: 3 residues within 4Å: Chain A: H.693, V.694, D.695 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.694 Salt bridges: A:D.695 DMS.10: 5 residues within 4Å: Chain A: N.280, I.290, S.293, R.296, E.769 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.769

1 x X4I: N~2~-(3,5-difluorophenyl)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]glycinamide(Non-covalent)

X4I.6: 23 residues within 4Å: Chain A: T.112, Q.124, E.126, A.127, N.265, V.266, G.267, A.268, M.269, E.270, H.303, E.304, H.307, E.326, M.378, E.379, Y.382, T.383, T.384, Y.387, M.841 Ligands: GOL.1, ZN.12 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.266, A:V.266, A:Y.382, A:Y.382, A:Y.387 Hydrogen bonds: A:G.267, A:A.268, A:Y.387, A:Y.387 Water bridges: A:R.296 pi-Stacking: A:Y.382 Halogen bonds: A:N.265, A:M.378

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain A: H.303, H.307, E.326 Ligands: X4I.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.303, A:H.307, A:E.326, A:E.326

4 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 1 residues within 4Å: Chain A: E.764 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain A: G.57 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.57, H2O.10, H2O.21, H2O.21, H2O.27, H2O.31 MG.15: 1 residues within 4Å: Chain A: D.245 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain A: N.890 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Calic, P.P.S. et al., Structure-based development of potent Plasmodium falciparum M1 and M17 aminopeptidase selective and dual inhibitors via S1'-region optimisation. Eur.J.Med.Chem. (2022)

Release Date

2023-01-18

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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