SMTL ID : 4zx6.1

X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 10s

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.302, H.306, E.325 Ligands: 4U6.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.302, A:H.306, A:E.325, A:E.325, 4U6.2

1 x 4U6: N-{(1R)-2-(hydroxyamino)-1-[3'-(N'-hydroxycarbamimidoyl)biphenyl-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide(Covalent)

4U6.2: 19 residues within 4Å: Chain A: E.125, A.126, V.265, G.266, A.267, E.269, R.295, H.302, E.303, H.306, E.325, E.378, N.379, Y.381, Y.386, M.840 Ligands: ZN.1, DMS.5, DMS.6 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.265, A:V.265, A:E.378, A:Y.381, A:Y.381, A:Y.386 Hydrogen bonds: A:G.266, A:A.267, A:A.267, A:Y.386, A:Y.386 Water bridges: A:E.269, A:K.324 pi-Stacking: A:Y.381

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.244 No protein-ligand interaction detected (PLIP)

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 3 residues within 4Å: Chain A: V.51, D.53, F.81 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.53 DMS.5: 6 residues within 4Å: Chain A: Y.381, T.382, T.383, Y.386 Ligands: 4U6.2, DMS.6 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.386 DMS.6: 7 residues within 4Å: Chain A: N.379, Y.381, T.843, Q.844, Y.883 Ligands: 4U6.2, DMS.5 No protein-ligand interaction detected (PLIP) DMS.8: 7 residues within 4Å: Chain A: Q.479, Y.480, T.481, K.490, K.491, P.492, E.521 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.481, A:T.481

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: V.158, K.165, H.200, Y.217, F.219, R.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.165, A:R.254, A:R.254

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drinkwater, N. et al., Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions. Eur.J.Med.Chem. (2016)

Release Date

2016-03-30

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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