SMTL ID : 4k5m.1

Phosphonic Arginine Mimetics as Inhibitors of the M1 Aminopeptidases from Plasmodium falciparum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.303, H.307, E.326 Ligands: 1OV.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.303, A:H.307, A:E.326, A:E.326

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: G.57 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:G.57, H2O.6, H2O.42, H2O.42, H2O.42, H2O.42 MG.3: 1 residues within 4Å: Chain A: E.764 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: Y.572, C.575, T.576, Y.579, Y.630, S.633, L.634, P.635 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.633, A:S.633 GOL.5: 10 residues within 4Å: Chain A: K.286, Y.687, F.688, H.693, V.694, D.695, Q.698, M.699, R.702, Y.732 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:K.286, A:Y.687, A:D.695, A:D.695, A:R.702, A:R.702, A:Y.732 Water bridges: A:Y.687 GOL.7: 7 residues within 4Å: Chain A: T.299, V.300, H.303, V.330, E.333, Y.387 Ligands: 1OV.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.333 Water bridges: A:R.296

1 x 1OV: [(1R)-1-amino-4-carbamimidamidobutyl]phosphonic acid(Non-covalent)

1OV.6: 13 residues within 4Å: Chain A: E.126, A.268, M.269, E.270, H.303, E.304, H.307, K.325, E.326, Y.382, Y.387 Ligands: ZN.1, GOL.7 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.126, A:A.268, A:A.268, A:Y.387 Water bridges: A:A.127, A:A.127 pi-Cation interactions: A:Y.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kannan Sivaraman, K. et al., Synthesis and Structure-Activity Relationships of Phosphonic Arginine Mimetics as Inhibitors of the M1 and M17 Aminopeptidases from Plasmodium falciparum. J.Med.Chem. (2013)

Release Date

2013-06-12

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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