SMTL ID : 6ee4.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 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: J4S.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, J4S.2

1 x J4S: (2R)-2-[(cyclopropylacetyl)amino]-N-hydroxy-2-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)acetamide(Non-covalent)

J4S.2: 21 residues within 4Å: Chain A: T.110, Q.122, E.124, A.125, N.263, V.264, G.265, A.266, M.267, E.268, H.301, E.302, H.305, E.324, M.376, E.377, Y.380, Y.385, M.839 Ligands: ZN.1, PO4.9 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.264, A:V.264, A:Y.380, A:Y.385 Hydrogen bonds: A:G.265, A:A.266, A:A.266, A:Y.385 pi-Stacking: A:Y.380 Halogen bonds: A:N.263

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 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.4: 6 residues within 4Å: Chain A: A.108, T.110, R.130, E.377, P.838, N.878 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.110 Water bridges: A:R.130, A:R.130, A:M.839, A:N.878 GOL.5: 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, A:Y.730 GOL.6: 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:N.378, A:T.382, A:Q.843, A:K.849, A:R.885 GOL.7: 10 residues within 4Å: Chain A: D.350, Y.570, C.573, T.574, Y.577, Y.628, I.629, S.631, L.632, P.633 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.570, A:Y.628 Water bridges: A:D.350, A:D.350, A:Q.634, A:Q.634

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

PO4.8: 1 residues within 4Å: Chain A: N.78 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.78 Water bridges: A:G.55 PO4.9: 6 residues within 4Å: Chain A: R.294, H.301, E.302, E.331, Y.385 Ligands: J4S.2 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.294, A:T.297, A:T.297 Salt bridges: A:R.294, A:H.301 PO4.10: 6 residues within 4Å: Chain A: H.458, K.481, Y.546, E.548, N.640, F.641 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.640, A:N.640 Water bridges: A:K.481, A:K.481, A:K.481, A:Y.546 Salt bridges: A:H.458, A:K.481

5 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 1 residues within 4Å: Chain A: E.762 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain A: D.243 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain A: E.331 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.331, H2O.20, H2O.26, H2O.34, H2O.49 MG.14: 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.18, H2O.24, H2O.32, H2O.46 MG.15: 1 residues within 4Å: Chain A: N.888 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

Related Entries With Identical Sequence