SMTL ID : 5xm7.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 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: 89X.16 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)(Non-functional Binders)

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.5, H2O.11, H2O.13 MG.3: 2 residues within 4Å: Chain A: E.786 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: Y.682, S.732, L.733, K.736 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.732 GOL.6: 4 residues within 4Å: Chain A: N.488, Q.495, S.497 Ligands: GOL.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.488, A:N.488, A:S.497 GOL.7: 6 residues within 4Å: Chain A: K.486, Y.487, N.488, S.497, H.499 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.497, A:H.499 GOL.8: 6 residues within 4Å: Chain A: S.750, K.751, S.752, P.753, W.758, L.781 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.750 Water bridges: A:K.777 GOL.9: 6 residues within 4Å: Chain A: L.789, V.815, L.816, S.819, D.824 Ligands: MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.816, A:S.819 Water bridges: A:S.819, A:D.824, A:D.824, A:D.824 GOL.10: 8 residues within 4Å: Chain A: N.287, V.288, G.289, N.300, N.302, N.823, R.826, Q.867 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.288, A:N.302, A:N.302, A:R.826 Water bridges: A:R.318 GOL.11: 4 residues within 4Å: Chain A: V.74, D.76, F.104, I.159 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.76, A:D.76 GOL.12: 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:Q.502, A:T.504, A:T.504, A:K.513 GOL.13: 4 residues within 4Å: Chain A: H.482, Y.570, N.664, F.665 No protein-ligand interaction detected (PLIP) GOL.14: 4 residues within 4Å: Chain A: L.606, F.665, V.666, S.667 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.667, A:S.667 GOL.15: 3 residues within 4Å: Chain A: T.44, V.59, D.61 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.169, A:D.169

1 x 89X: (2S)-4-methyl-N-[(1R)-2-(oxidanylamino)-2-oxidanylidene-1-phenyl-ethyl]-2-[(phenylmethyl)carbamoylamino]pentanamide(Non-covalent)

89X.16: 14 residues within 4Å: Chain A: E.148, V.288, G.289, A.290, E.292, H.325, E.326, H.329, E.348, Y.404, T.405, T.406, Y.409 Ligands: ZN.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.288, A:V.288, A:Y.404 Hydrogen bonds: A:G.289, A:A.290, A:A.290, A:E.326, A:Y.409

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

2018-06-20

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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