SMTL ID : 8ex3.1

Plasmodium falciparum M1 in complex with inhibitor 9aa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.303, H.307, E.326 Ligands: X10.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.303, A:H.307, A:E.326, A:E.326

1 x X10: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-N~2~-phenylglycinamide(Non-covalent)

X10.2: 20 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, E.379, Y.382, T.383, Y.387, M.841 Ligands: ZN.1 12 PLIP interactions: 12 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

5 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 1 residues within 4Å: Chain A: E.764 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: E.333 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.333, H2O.5, H2O.7, H2O.20, H2O.32, H2O.41 MG.5: 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.19, H2O.29, H2O.30, H2O.33 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: N.890 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 6 residues within 4Å: Chain A: A.110, T.112, R.132, E.379, P.840, N.880 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.112, A:T.112 Water bridges: A:R.132, A:M.841, A:S.878, A:N.880 GOL.9: 8 residues within 4Å: Chain A: V.266, G.267, N.278, N.280, S.281, R.296, N.801, R.804 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.10: 5 residues within 4Å: Chain A: N.380, Y.382, T.383, T.844, Y.884 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.380, A:T.844 Water bridges: A:Y.382, A:Y.382, A:T.384, A:Q.845, A:Q.845, A:Y.884

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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