SMTL ID : 4zw6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x 4SY: tert-butyl {(1S)-2-(hydroxyamino)-1-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-2-oxoethyl}carbamate(Non-covalent)

4SY.1: 19 residues within 4Å: Chain A: T.111, Q.123, E.125, A.126, V.265, G.266, A.267, E.269, R.295, V.299, H.302, E.303, H.306, E.325, Y.381, Y.386, M.840 Ligands: ZN.2, GOL.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.265, A:V.265, A:V.299, A:H.302, A:Y.381 Hydrogen bonds: A:A.126, A:G.266, A:A.267, A:A.267, A:A.267, A:E.303, A:Y.386 Water bridges: A:R.295 pi-Stacking: A:Y.381

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.302, H.306, E.325 Ligands: 4SY.1 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, 4SY.1

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

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: E.485 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.485, H2O.12, H2O.23, H2O.29 MG.5: 1 residues within 4Å: Chain A: E.763 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: V.265, G.266, N.277, N.279, S.280, R.295, N.800, R.803 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.277, A:N.279, A:S.280, A:R.295, A:R.803, A:R.803 Water bridges: A:G.266 GOL.7: 4 residues within 4Å: Chain A: Y.381, T.382, Y.386 Ligands: 4SY.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.382 Water bridges: A:T.383 GOL.8: 6 residues within 4Å: Chain A: Y.659, S.709, L.710, K.713, Y.744 Ligands: DMS.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.709, A:Y.744 Water bridges: A:K.655

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

DMS.9: 5 residues within 4Å: Chain A: N.379, Y.381, T.382, T.843, Q.844 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.360, A:T.383 DMS.10: 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.11: 6 residues within 4Å: Chain A: S.632, Y.659, T.706, S.709, L.710 Ligands: GOL.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.709 DMS.12: 4 residues within 4Å: Chain A: S.628, Y.629, S.632, T.706 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.632, A:T.706 pi-Cation interactions: A:Y.629

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

PO4.13: 4 residues within 4Å: Chain A: V.51, F.52, D.53, F.81 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.51, A:D.53, A:D.53 Water bridges: A:V.51 PO4.14: 5 residues within 4Å: Chain A: S.202, A.203, T.204, E.215, Y.217 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.202, A:T.204, A:T.204

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

Related Entries With Identical Sequence