SMTL ID : 5y1h.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

monomer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.6, H2O.18, H2O.20 MG.2: 2 residues within 4Å: Chain A: E.355 Ligands: GOL.6 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.355, H2O.4, H2O.9, H2O.15, H2O.18, H2O.21 MG.3: 1 residues within 4Å: Chain A: E.786 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: H.325, H.329, E.348 Ligands: E8C.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.325, A:H.329, A:E.348, A:E.348

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: Y.682, S.732, L.733, K.736, Y.767 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.732, A:Y.767 GOL.6: 9 residues within 4Å: Chain A: G.289, A.290, R.318, V.322, H.325, E.326, Y.409 Ligands: MG.2, E8C.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.290, A:R.318, A:E.326 Water bridges: A:E.355 GOL.7: 6 residues within 4Å: Chain A: E.401, N.402, Y.404, T.866, Q.867, Y.906 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.401, A:T.866, A:T.866 Water bridges: A:K.873, A:K.873

1 x E8C: (2R)-2-[[2,4-bis(fluoranyl)phenyl]methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide(Non-covalent)

E8C.8: 18 residues within 4Å: Chain A: Q.146, E.148, V.288, G.289, A.290, M.291, E.292, R.318, H.325, E.326, H.329, E.348, Y.404, Y.409, R.826, Q.867 Ligands: ZN.4, GOL.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.148, A:V.288, A:Y.404 Hydrogen bonds: A:G.289, A:A.290, A:A.290, A:Y.409, A:Y.409 Water bridges: A:Y.409

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-(2,4-difluorobenzyl)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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