SMTL ID : 4r5x.1

Structure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor

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.315, H.319, E.338 Ligands: R5X.7 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.315, A:H.319, A:E.338, A:E.338

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: V.278, G.279, N.290, N.292, S.293, R.308, N.813, R.816 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.290, A:N.292, A:R.308, A:R.308, A:R.816, A:R.816 Water bridges: A:Q.857 GOL.3: 7 residues within 4Å: Chain A: M.352, T.353, V.706, D.707, F.708, D.709 Ligands: DMS.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.708, A:D.709, A:D.709 Water bridges: A:V.706, A:V.706 GOL.4: 6 residues within 4Å: Chain A: Y.394, T.395, T.396, Y.399, D.400 Ligands: R5X.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Y.394, A:D.400, A:D.400 GOL.6: 10 residues within 4Å: Chain A: K.298, Y.699, F.700, H.705, V.706, D.707, Q.710, M.711, R.714, Y.744 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.298, A:Y.699, A:D.707, A:D.707, A:R.714, A:R.714 Water bridges: A:Y.744

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 1 residues within 4Å: Chain A: G.69 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.69, H2O.7, H2O.8, H2O.11, H2O.11, H2O.33

1 x R5X: 3-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide(Non-covalent)

R5X.7: 18 residues within 4Å: Chain A: E.138, A.139, V.278, G.279, A.280, M.281, E.282, R.308, H.315, E.316, H.319, E.338, E.391, Y.394, Y.399, M.853 Ligands: ZN.1, GOL.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.278, A:V.278, A:V.278, A:Y.394, A:Y.394 Hydrogen bonds: A:G.279, A:A.280, A:A.280, A:R.308, A:Y.399, A:Y.399 Water bridges: A:E.316, A:E.316, A:E.345, A:E.345, A:E.345, A:E.345 pi-Stacking: A:Y.394 pi-Cation interactions: A:R.308

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

DMS.8: 5 residues within 4Å: Chain A: N.392, Y.394, T.856, Q.857, Y.896 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.896 DMS.9: 6 residues within 4Å: Chain A: Y.672, S.722, L.723, K.726, Y.757 Ligands: DMS.10 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.672 DMS.10: 7 residues within 4Å: Chain A: V.644, S.645, Y.672, T.719, S.722, L.723 Ligands: DMS.9 No protein-ligand interaction detected (PLIP) DMS.11: 5 residues within 4Å: Chain A: V.64, F.65, D.66, F.94, I.149 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.66 DMS.12: 4 residues within 4Å: Chain A: H.705, V.706, D.707 Ligands: GOL.3 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.707

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mistry, S.N. et al., Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors. J.Med.Chem. (2014)

Release Date

2014-10-29

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase