SMTL ID : 5y1t.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.325, H.329, E.348 Ligands: E8G.5, GOL.7 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 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.79, H2O.3, H2O.11, H2O.13 MG.3: 2 residues within 4Å: Chain A: E.355 Ligands: GOL.7 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.355, H2O.1, H2O.3, H2O.8, H2O.13 MG.4: 2 residues within 4Å: Chain A: E.786, D.824 No protein-ligand interaction detected (PLIP)

1 x E8G: (2S)-2-[(2,3-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide(Non-covalent)

E8G.5: 19 residues within 4Å: Chain A: Q.146, E.148, N.287, V.288, G.289, A.290, M.291, E.292, H.325, E.326, H.329, E.348, E.401, Y.404, Y.409, M.863 Ligands: ZN.1, GOL.7, GOL.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:N.287, A:V.288, A:V.288, A:E.401, A:E.401, A:Y.404, A:Y.409 Hydrogen bonds: A:A.290, A:Y.409, A:Y.409

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: S.750, K.751, S.752, P.753, W.758, L.781 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.750 Water bridges: A:N.310, A:K.777 GOL.7: 9 residues within 4Å: Chain A: V.322, H.325, E.326, E.355, Y.409 Ligands: ZN.1, MG.3, E8G.5, GOL.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.326 Water bridges: A:G.289, A:H.325, A:E.355 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: 6 residues within 4Å: Chain A: Y.404, T.405, T.406, Y.409 Ligands: E8G.5, GOL.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.406, A:D.410, A:D.410

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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