SMTL ID : 4zx4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 4TL: N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluorobiphenyl-4-yl)ethyl]-2,2-dimethylpropanamide(Non-covalent)

4TL.1: 20 residues within 4Å: Chain A: T.111, Q.123, E.125, A.126, N.264, V.265, G.266, A.267, E.269, R.295, H.302, E.303, H.306, E.325, M.377, E.378, Y.381, Y.386, M.840 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.265, A:V.265, A:Y.381, A:Y.386 Hydrogen bonds: A:G.266, A:A.267, A:A.267, A:Y.386, A:Y.386 pi-Stacking: A:Y.381 Halogen bonds: A:M.377

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.302, H.306, E.325 Ligands: 4TL.1 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, 4TL.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: E.763 No protein-ligand interaction detected (PLIP)

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

PO4.4: 3 residues within 4Å: Chain A: E.505, N.506, Y.563 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: N.379, Y.381, T.382, T.843, Q.844, Y.883 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.379, A:Y.381, A:T.843 Water bridges: A:E.360, A:Q.844, A:Y.883, A:R.886 GOL.6: 5 residues within 4Å: Chain A: H.459, K.482, Y.547, N.641, F.642 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.482 Water bridges: A:H.459, A:E.549 GOL.7: 6 residues within 4Å: Chain A: Y.659, S.709, L.710, K.713, Y.744 Ligands: DMS.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.709, A:Y.744 Water bridges: A:K.655

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

DMS.8: 4 residues within 4Å: Chain A: D.564, S.565, A.567, R.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.570 DMS.9: 4 residues within 4Å: Chain A: S.628, Y.629, S.632, T.706 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.632, A:T.706 pi-Cation interactions: A:Y.629 DMS.10: 7 residues within 4Å: Chain A: V.631, S.632, Y.659, T.706, S.709, L.710 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.709

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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