SMTL ID : 4qir.1

Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-2-(pyridin-3-yl)ethylGlyP[CH2]Phe

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x 379: 3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid(Non-covalent)

379.1: 24 residues within 4Å: Chain A: Q.118, E.120, P.121, M.259, G.260, A.261, M.262, E.263, S.292, V.293, H.296, E.297, H.300, K.318, E.319, V.323, D.326, N.372, Y.375, Y.380, E.381, Q.821 Ligands: GOL.6, ZN.9 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.293, A:H.296, A:V.323, A:Y.375, A:Y.380, A:Y.380 Hydrogen bonds: A:G.260, A:A.261, A:A.261, A:E.297, A:K.318, A:E.319, A:N.372, A:Y.380 pi-Stacking: A:Y.375 pi-Cation interactions: A:H.296

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: M.472, T.473, D.474 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.473, A:T.473, A:D.474 GOL.3: 10 residues within 4Å: Chain A: N.658, R.682, R.686, V.689, L.690, H.696, V.700, K.703, M.707, I.717 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.658, A:R.682, A:R.682, A:R.686, A:R.686 Water bridges: A:K.703, A:K.703 GOL.4: 4 residues within 4Å: Chain A: Y.199, F.200, T.201, K.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.199, A:T.201, A:K.230 GOL.6: 6 residues within 4Å: Chain A: Y.375, T.376, M.377, Y.380, E.381 Ligands: 379.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.380 GOL.7: 3 residues within 4Å: Chain A: E.628, N.834, K.835 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.835 GOL.8: 7 residues within 4Å: Chain A: R.729, N.730, L.733, A.734, Y.750, V.754, Q.765 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.730, A:Q.765

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 6 residues within 4Å: Chain A: D.25, L.26, H.27, K.38, S.39, R.40 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.25, A:R.40 Water bridges: A:R.40 pi-Cation interactions: A:R.40

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain A: H.296, H.300, E.319, Y.380 Ligands: 379.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.296, A:H.300, A:E.319, A:E.319

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 4 residues within 4Å: Chain A: R.639, L.643, R.691, R.758 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.639 Salt bridges: A:R.639, A:R.758

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vassiliou, S. et al., Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases. J.Med.Chem. (2014)

Release Date

2014-09-24

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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