SMTL ID : 8ez2.1

Plasmodium falciparum M1 in complex with inhibitor 15ag

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 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 9 PLIP interactions: 9 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, A:Y.732 GOL.5: 7 residues within 4Å: Chain A: N.265, V.266, G.267, R.296, Q.845 Ligands: X68.3, GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.267, A:R.296, A:R.296 GOL.6: 9 residues within 4Å: Chain A: V.266, G.267, N.278, N.280, S.281, R.296, N.801, R.804 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.278, A:N.280, A:S.281, A:R.296, A:R.804 GOL.7: 6 residues within 4Å: Chain A: S.363, H.460, K.483, Y.548, N.642, F.643 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.460, A:K.483 Water bridges: A:E.550 GOL.8: 5 residues within 4Å: Chain A: I.290, L.737, T.738, S.741, T.773 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.741, A:S.741 Water bridges: A:E.769, A:K.772 GOL.9: 6 residues within 4Å: Chain A: K.118, S.262, E.764, Q.768, N.799, D.802 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.262, A:E.764, A:Q.768, A:N.799, A:D.802 Water bridges: A:K.118, A:D.263, A:D.263, A:D.263

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

DMS.2: 4 residues within 4Å: Chain A: V.500, Q.514, T.515, R.541 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.541 DMS.4: 7 residues within 4Å: Chain A: Y.572, T.576, Y.579, Y.630, S.633, L.634, P.635 No protein-ligand interaction detected (PLIP)

1 x X68: N-[(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]-N~2~-(3-fluorophenyl)glycinamide(Non-covalent)

X68.3: 16 residues within 4Å: Chain A: E.126, A.127, V.266, G.267, A.268, E.270, H.303, E.304, H.307, E.326, Y.382, T.383, T.384, Y.387 Ligands: GOL.5, ZN.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.266, A:V.266, A:V.266, 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

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain A: H.303, H.307, E.326 Ligands: X68.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.303, A:H.307, A:E.326, A:E.326

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 1 residues within 4Å: Chain A: G.57 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.57, H2O.13, H2O.20, H2O.24 MG.12: 2 residues within 4Å: Chain A: E.486, 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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