SMTL ID : 8eyf.1

Plasmodium falciparum M1 in complex with inhibitor 15aa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: K.286, Y.687, H.693, V.694, D.695, Q.698, M.699, R.702, Y.732 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.286, A:Y.687, A:D.695, A:D.695, A:R.702, A:R.702 Water bridges: A:Q.698 GOL.4: 6 residues within 4Å: Chain A: E.379, N.380, Y.382, T.383, T.844, Y.884 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.380 Water bridges: A:K.851, A:R.887 GOL.5: 6 residues within 4Å: Chain A: G.164, D.165, D.183, P.185, L.253, S.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.183, A:S.254, A:S.254 GOL.6: 6 residues within 4Å: Chain A: W.231, K.238, M.340, S.692, V.694, F.696 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.340, A:S.692, A:V.694, A:V.694 GOL.7: 5 residues within 4Å: Chain A: Y.206, K.209, A.241, E.244, D.245 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.206, A:E.244 GOL.9: 6 residues within 4Å: Chain A: V.300, H.303, E.304, E.333, Y.387 Ligands: X4T.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.304, A:E.333 Water bridges: A:R.296, A:R.296 GOL.10: 5 residues within 4Å: Chain A: S.633, Y.660, T.707, S.710, L.711 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.660, A:Y.660, A:S.710 GOL.11: 7 residues within 4Å: Chain A: L.360, R.638, T.811, N.812, E.848, P.849, L.852 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.811, A:T.811 Water bridges: A:R.638, A:E.848

1 x X4T: N-[(1R)-1-(4-bromophenyl)-2-(hydroxyamino)-2-oxoethyl]-N~2~-phenylglycinamide(Non-covalent)

X4T.2: 15 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, Y.387 Ligands: GOL.9, ZN.12 10 PLIP interactions: 10 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

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

DMS.3: 5 residues within 4Å: Chain A: M.143, L.186, N.312, R.313, G.419 No protein-ligand interaction detected (PLIP) DMS.8: 5 residues within 4Å: Chain A: A.295, T.343, T.345, T.346, F.696 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 4 residues within 4Å: Chain A: H.303, H.307, E.326 Ligands: X4T.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.303, A:H.307, A:E.326, A:E.326

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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