SMTL ID : 6ee6.1

X-ray crystal structure of Pf-M1 in complex with inhibitor (6o) and catalytic zinc ion

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: J4P.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.301, A:H.305, A:E.324, A:E.324, J4P.2

1 x J4P: (2R)-2-[(cyclopentylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide(Non-covalent)

J4P.2: 23 residues within 4Å: Chain A: T.110, Q.122, E.124, A.125, N.263, V.264, G.265, A.266, E.268, R.294, T.297, V.298, H.301, E.302, H.305, E.324, M.376, E.377, Y.380, Y.385, M.839 Ligands: ZN.1, GOL.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.264, A:V.264, A:T.297, A:V.298, A:H.301, A:Y.380 Hydrogen bonds: A:G.265, A:A.266, A:A.266, A:Y.385, A:Y.385 pi-Stacking: A:Y.380 Halogen bonds: A:M.376

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: V.50, D.52, F.80, I.135 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.136, A:D.136 GOL.4: 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:Y.380, A:T.842 Water bridges: A:E.359, A:Q.843, A:Q.843, A:Y.882, A:R.885 GOL.5: 5 residues within 4Å: Chain A: Y.380, T.381, T.382, Y.385 Ligands: J4P.2 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.265, A:Y.380, A:T.382 GOL.6: 8 residues within 4Å: Chain A: V.264, G.265, N.276, N.278, S.279, R.294, N.799, R.802 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.276, A:N.278, A:N.278, A:S.279, A:S.279, A:R.294, A:R.802 Water bridges: A:Q.843 GOL.7: 3 residues within 4Å: Chain A: H.691, V.692, D.693 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.691 Water bridges: A:V.692, A:V.692, A:V.692, A:D.693 GOL.11: 6 residues within 4Å: Chain A: A.108, T.110, R.130, E.377, P.838, N.878 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.110, A:T.110, A:E.377 Water bridges: A:M.839 GOL.12: 8 residues within 4Å: Chain A: K.284, H.691, V.692, D.693, Q.696, M.697, R.700, Y.730 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.284, A:K.284, A:D.693, A:D.693, A:R.700, A:R.700, A:Y.730 Water bridges: A:Y.730 GOL.13: 8 residues within 4Å: Chain A: D.350, Y.570, C.573, T.574, Y.577, Y.628, S.631, P.633 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.628 Water bridges: A:D.350, A:Q.634

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

MG.8: 1 residues within 4Å: Chain A: G.55 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.55, H2O.16, H2O.25, H2O.30, H2O.33, H2O.33 MG.9: 1 residues within 4Å: Chain A: E.762 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vinh, N.B. et al., Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. (2019)

Release Date

2018-12-26

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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