SMTL ID : 4r5t.1

Structure of the m1 alanylaminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.308, H.312, E.331 Ligands: R5T.12 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.308, A:H.312, A:E.331, A:E.331, R5T.12

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

DMS.2: 5 residues within 4Å: Chain A: N.385, T.388, T.849, Q.850, Y.889 No protein-ligand interaction detected (PLIP) DMS.3: 6 residues within 4Å: Chain A: S.267, E.769, Q.773, S.802, N.804, D.807 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.804 Salt bridges: A:E.769, A:D.807

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: G.62, K.64, I.107, I.108, H.109 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.64, A:N.85, A:I.107, A:H.109 Water bridges: A:H.109 GOL.5: 7 residues within 4Å: Chain A: M.345, T.346, T.348, V.699, D.700, F.701, D.702 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.345, A:V.699, A:D.700, A:F.701, A:D.702, A:D.702 GOL.6: 5 residues within 4Å: Chain A: H.465, K.488, E.555, N.647, F.648 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.488, A:E.555, A:E.555 GOL.7: 5 residues within 4Å: Chain A: S.638, Y.665, T.712, S.715 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.715 Water bridges: A:L.639, A:Y.665 GOL.8: 6 residues within 4Å: Chain A: S.634, Y.635, S.638, T.708 Ligands: GOL.7, GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.634, A:S.638, A:S.638 GOL.9: 8 residues within 4Å: Chain A: V.271, G.272, N.283, N.285, S.286, R.301, N.806, R.809 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.283, A:N.285, A:S.286, A:R.301, A:R.809, A:R.809 Water bridges: A:G.272, A:Q.850 GOL.10: 3 residues within 4Å: Chain A: K.347, D.629, D.702 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.347 Water bridges: A:A.628, A:A.630 GOL.11: 9 residues within 4Å: Chain A: Y.577, C.580, T.581, Y.584, Y.635, S.638, L.639, P.640 Ligands: GOL.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.581 Water bridges: A:Q.641

1 x R5T: tert-butyl {(1S)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}carbamate(Non-covalent)

R5T.12: 17 residues within 4Å: Chain A: E.131, A.132, V.271, G.272, A.273, E.275, R.301, V.305, H.308, E.309, H.312, E.331, E.384, Y.387, Y.392, M.846 Ligands: ZN.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.271, A:V.305, A:H.308, A:Y.387, A:Y.387 Hydrogen bonds: A:G.272, A:A.273, A:A.273, A:A.273, A:E.275, A:Y.392 Water bridges: A:E.275, A:R.301, A:Y.392 pi-Stacking: A:Y.387

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mistry, S.N. et al., Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors. J.Med.Chem. (2014)

Release Date

2014-10-29

Peptides

M1 family aminopeptidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

M1 family aminopeptidase