SMTL ID : 6ee3.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 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: J4V.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, J4V.2

1 x J4V: (1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide(Non-covalent)

J4V.2: 21 residues within 4Å: Chain A: T.110, Q.122, E.124, A.125, N.263, V.264, G.265, A.266, M.267, E.268, R.294, H.301, E.302, H.305, E.324, M.376, E.377, Y.380, Y.385, M.839 Ligands: ZN.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.264, A:V.264, A:Y.380 Hydrogen bonds: A:G.265, A:A.266, A:A.266, A:Y.385, A:Y.385 Water bridges: A:E.302 pi-Stacking: A:Y.380 Halogen bonds: A:E.377

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

PO4.3: 4 residues within 4Å: Chain A: P.503, E.504, N.505, Y.562 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.504

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: K.284, Y.685, F.686, H.691, V.692, D.693, Q.696, M.697, R.700, Y.730 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.284, A:Y.685, A:D.693, A:D.693, A:R.700, A:R.700 Water bridges: A:Y.730 GOL.5: 6 residues within 4Å: Chain A: S.732, L.735, T.736, S.739, T.771, R.774 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.732, A:S.739, A:S.739, A:R.774 Water bridges: A:E.767, A:T.771

4 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 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.10, H2O.19, H2O.19, H2O.23, H2O.29 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.762 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: N.888 No protein-ligand interaction detected (PLIP)

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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