SMTL ID : 4x2u.1

X-ray crystal structure of the orally available aminopeptidase inhibitor, Tosedostat, bound to the M1 Alanyl Aminopeptidase from P. falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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: TOD.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.301, A:H.305, A:E.324, A:E.324

1 x TOD: (2S)-({(2R)-2-[(1S)-1-hydroxy-2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}amino)(phenyl)ethanoic acid(Non-covalent)

TOD.2: 17 residues within 4Å: Chain A: N.263, V.264, G.265, A.266, E.268, R.294, V.298, H.301, E.302, H.305, E.324, Y.385, R.802, Q.843 Ligands: ZN.1, GOL.5, GOL.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.264, A:V.264, A:V.298, A:H.301, A:Y.385 Hydrogen bonds: A:G.265, A:A.266, A:A.266, A:Y.385 Water bridges: A:K.323, A:K.323, A:K.323, A:Y.385 Salt bridges: A:R.294

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 1 residues within 4Å: Chain A: G.55 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:G.55, H2O.3, H2O.4, H2O.5, H2O.11 MG.4: 1 residues within 4Å: Chain A: E.762 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain A: N.888 No protein-ligand interaction detected (PLIP)

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: Q.122, E.124, A.125, V.264, M.267, Y.380 Ligands: TOD.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.122, A:E.124, A:A.125 GOL.6: 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.7: 6 residues within 4Å: Chain A: V.630, S.631, Y.658, T.705, S.708, L.709 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.631, A:Y.658, A:Y.658, A:S.708, A:S.708 Water bridges: A:S.631 GOL.8: 5 residues within 4Å: Chain A: H.458, K.481, Y.546, N.640, F.641 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.481, A:K.481, A:Y.546 Water bridges: A:S.361, A:E.548 GOL.9: 6 residues within 4Å: Chain A: N.378, Y.380, T.381, T.842, Q.843, Y.882 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.378, A:T.842 Water bridges: A:E.359, A:K.849, A:K.849, A:K.849, A:Y.882 GOL.10: 5 residues within 4Å: Chain A: P.503, E.504, N.505, G.506, Y.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.503, A:N.505 GOL.11: 9 residues within 4Å: Chain A: D.350, Y.570, C.573, T.574, Y.577, Y.628, I.629, S.631, P.633 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.350, A:D.350, A:R.353, A:Q.634 GOL.12: 5 residues within 4Å: Chain A: Y.380, T.381, T.382, Y.385 Ligands: TOD.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.385

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drinkwater, N. et al., X-ray crystal structures of an orally available aminopeptidase inhibitor, Tosedostat, bound to anti-malarial drug targets PfA-M1 and PfA-M17. Proteins (2015)

Release Date

2015-02-18

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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