SMTL ID : 4zx5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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: 4TM.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, 4TM.2

1 x 4TM: N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(thiophen-3-yl)phenyl]ethyl}-2,2-dimethylpropanamide(Non-covalent)

4TM.2: 17 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, Y.381, Y.386, M.840 Ligands: ZN.1, DMS.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.265, A:V.265, 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:E.269 pi-Stacking: A:Y.381

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: G.56 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.56, H2O.7, H2O.17, H2O.18, H2O.24, H2O.25 MG.4: 1 residues within 4Å: Chain A: E.763 No protein-ligand interaction detected (PLIP)

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

DMS.5: 5 residues within 4Å: Chain A: E.378, N.379, Y.381, T.843, Q.844 No protein-ligand interaction detected (PLIP) DMS.6: 5 residues within 4Å: Chain A: Y.381, T.382, T.383, Y.386 Ligands: 4TM.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:D.387 pi-Cation interactions: A:Y.386

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: Y.205, K.208, A.240, E.243, D.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.205, A:A.240

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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