SMTL ID : 5y1v.1

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,6-diethylphenyl)ureido)- N-hydroxy-4-methylpentanamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 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: 8LO.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.325, A:H.329, A:E.348, A:E.348

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: G.79 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.79, H2O.19, H2O.20 MG.3: 1 residues within 4Å: Chain A: E.786 No protein-ligand interaction detected (PLIP)

1 x 8LO: (2R)-2-[(2,6-diethylphenyl)carbamoylamino]-4-methyl-N-oxidanyl-pentanamide(Non-covalent)

8LO.4: 15 residues within 4Å: Chain A: Q.146, E.148, V.288, G.289, A.290, M.291, E.292, H.325, E.326, H.329, E.348, Y.404, Y.409 Ligands: ZN.1, GOL.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.148, A:V.288, A:V.288, A:Y.404, A:Y.404, A:Y.409, A:Y.409 Hydrogen bonds: A:G.289, A:A.290, A:A.290, A:Y.409, A:Y.409 Water bridges: A:E.326 pi-Stacking: A:Y.409

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: H.325, V.352, E.355 Ligands: 8LO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.325, A:E.355 GOL.6: 5 residues within 4Å: Chain A: N.488, D.490, Q.495, Y.496, S.497 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.488, A:D.490, A:K.493, A:K.493, A:Q.495 Water bridges: A:D.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marapaka, A.K. et al., Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,6-diethylphenyl)ureido)- N-hydroxy-4-methylpentanamide. To Be Published

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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