SMTL ID : 6eab.1

X-ray crystal structure of Pf-M1 in complex with inhibitor (6j) and catalytic zinc ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.301, H.305, E.324 Ligands: J2D.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.301, A:H.305, A:E.324, A:E.324, J2D.2

1 x J2D: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]oxane-4-carboxamide(Non-covalent)

J2D.2: 22 residues within 4Å: Chain A: T.110, Q.122, E.124, A.125, N.263, V.264, G.265, A.266, E.268, R.294, V.298, H.301, E.302, H.305, E.324, M.376, E.377, Y.380, Y.385, M.839 Ligands: ZN.1, GOL.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.264, A:V.264, A:Y.380, A:Y.385 Hydrogen bonds: A:G.265, A:A.266, A:A.266, A:Y.385 Water bridges: A:R.294 pi-Stacking: A:Y.380 Halogen bonds: A:N.263, A:M.376

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.264, Y.380, T.381, T.382, Y.385, D.386 Ligands: J2D.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.386 GOL.4: 6 residues within 4Å: Chain A: A.108, T.110, R.130, E.377, P.838, N.878 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.110, A:N.878 Water bridges: A:R.130

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: G.55 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.55, H2O.11, H2O.21, H2O.23, H2O.27, H2O.27 MG.6: 1 residues within 4Å: Chain A: E.762 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: D.243 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: E.331 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.331, H2O.11, H2O.22, H2O.23, H2O.28, H2O.39

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.9: 4 residues within 4Å: Chain A: N.378, Y.380, T.842, Y.882 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.882 Water bridges: A:Y.380, A:Y.380, A:Y.380, A:Q.843, A:K.849

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinh, N.B. et al., Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. (2019)

Release Date

2018-12-26

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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