SMTL ID : 4zw8.1

X-ray crystal structure of PfA-M1 in complex with hydroxamic acid-based inhibitor 9r

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.302, H.306, E.325 Ligands: 4T2.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.302, A:H.306, A:E.325, A:E.325, 4T2.2

1 x 4T2: tert-butyl {(1S)-2-(hydroxyamino)-1-[3'-(N'-hydroxycarbamimidoyl)biphenyl-4-yl]-2-oxoethyl}carbamate(Non-covalent)

4T2.2: 20 residues within 4Å: Chain A: L.110, T.111, Q.123, E.125, A.126, N.264, V.265, G.266, A.267, E.269, R.295, H.302, E.303, H.306, E.325, Y.381, Y.386, M.840 Ligands: ZN.1, GOL.8 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:V.265, A:V.265, A:H.302, A:Y.381, A:Y.386 Hydrogen bonds: A:E.125, A:N.264, A:G.266, A:A.267, A:A.267, A:A.267, A:E.303, A:Y.386 Water bridges: A:T.127, A:N.264, A:N.264, A:N.264, A:N.264, A:R.295 pi-Stacking: A:Y.381

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

DMS.3: 6 residues within 4Å: Chain A: N.379, Y.381, T.382, T.843, Q.844, Y.883 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.360 DMS.4: 4 residues within 4Å: Chain A: D.564, S.565, A.567, R.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.570 DMS.5: 7 residues within 4Å: Chain A: V.631, S.632, Y.659, T.706, S.709, L.710 Ligands: DMS.6 No protein-ligand interaction detected (PLIP) DMS.6: 4 residues within 4Å: Chain A: Y.659, S.709, L.710 Ligands: DMS.5 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.659

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: H.459, Y.547, N.641, F.642 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.547 Water bridges: A:K.482 GOL.8: 4 residues within 4Å: Chain A: Y.381, T.382, Y.386 Ligands: 4T2.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.381, A:T.382

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Drinkwater, N. et al., Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions. Eur.J.Med.Chem. (2016)

Release Date

2016-03-30

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase

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