SMTL ID : 5y1k.1

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2-chlorobenzyl)ureido)-N-hydroxy-4-methylpentanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.325, H.329, E.348 Ligands: B1B.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.325, A:H.329, A:E.348, A:E.348

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: G.79 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.79, H2O.3, H2O.15, H2O.15, H2O.18 MG.3: 2 residues within 4Å: Chain A: E.355 Ligands: GOL.7 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.355, H2O.1, H2O.2, H2O.9, H2O.15, H2O.17 MG.4: 1 residues within 4Å: Chain A: E.786 No protein-ligand interaction detected (PLIP)

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: M.362, T.363, K.364, H.715, V.716, D.717, F.718, D.719 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.717, A:D.717, A:F.718, A:D.719 Water bridges: A:H.715, A:V.716 GOL.6: 7 residues within 4Å: Chain A: E.401, N.402, Y.404, T.405, T.866, Q.867, Y.906 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.401, A:T.866 Water bridges: A:E.383, A:K.873 GOL.7: 9 residues within 4Å: Chain A: G.289, A.290, R.318, V.322, H.325, E.326, Y.409 Ligands: MG.3, B1B.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.290, A:R.318, A:H.325, A:E.326, A:E.326 GOL.8: 5 residues within 4Å: Chain A: Y.682, S.732, L.733, K.736, Y.767 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.682, A:S.732, A:Y.767 GOL.9: 7 residues within 4Å: Chain A: Q.502, Y.503, T.504, K.513, K.514, P.515, E.544 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.504, A:T.504, A:E.544 Water bridges: A:K.513 GOL.10: 4 residues within 4Å: Chain A: N.488, D.490, Q.495, S.497 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.490, A:D.490, A:D.490, A:S.497

1 x B1B: (2S)-2-[(2-chlorophenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide(Non-covalent)

B1B.11: 17 residues within 4Å: Chain A: Q.146, E.148, A.149, V.288, G.289, A.290, E.292, H.325, E.326, H.329, E.348, E.401, Y.404, Y.409, M.863 Ligands: ZN.1, GOL.7 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.288, A:V.288, A:E.401, A:Y.404 Hydrogen bonds: A:Q.146, A:A.290, A:Y.409, A:Y.409 pi-Stacking: A:Y.404

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marapaka, A.K. et al., Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization. Chin.Chem.Lett. (2022)

Release Date

2018-08-01

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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