SMTL ID : 8ewz.1

Plasmodium falciparum M1 in complex with inhibitor 9c

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x X0I: (2R)-2-(cyclopentylcarbamamido)-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide(Non-covalent)

X0I.1: 22 residues within 4Å: Chain A: L.111, 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, Y.387, M.841 Ligands: DMS.2, ZN.7 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Q.124, A:V.266, A:Y.382, A:Y.387, A:Y.387 Hydrogen bonds: A:G.267, A:A.268, A:Y.387, A:Y.387 Water bridges: A:R.296, A:R.296 pi-Stacking: A:Y.382 Halogen bonds: A:L.111, A:N.265, A:M.378

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

DMS.2: 6 residues within 4Å: Chain A: R.296, V.300, H.303, E.304, Y.387 Ligands: X0I.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.296 Water bridges: A:R.296 Salt bridges: A:E.304, A:E.333 pi-Cation interactions: A:H.303

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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:S.281, A:S.281, A:R.296, A:R.804, 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.687 GOL.5: 6 residues within 4Å: Chain A: A.110, T.112, R.132, E.379, P.840, N.880 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.112, A:T.112, A:E.379 Water bridges: A:R.132, A:R.132 GOL.6: 6 residues within 4Å: Chain A: N.380, Y.382, T.383, T.844, Q.845, Y.884 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.380, A:T.844 Water bridges: A:Y.382, A:Q.845, A:Y.884, A:Y.884, A:Y.884, A:R.887, A:R.887

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 4 residues within 4Å: Chain A: H.303, H.307, E.326 Ligands: X0I.1 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)(Non-functional Binders)

MG.8: 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.8, H2O.15, H2O.21, H2O.29, H2O.39 MG.9: 1 residues within 4Å: Chain A: E.764 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 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.11, H2O.18, H2O.25, H2O.27, H2O.28

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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