SMTL ID : 4qme.1

Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x 37B: (2S)-3-[(S)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid(Non-covalent)

37B.1: 27 residues within 4Å: Chain A: M.102, Q.114, E.116, P.117, F.253, N.254, M.255, G.256, A.257, M.258, E.259, S.288, V.289, H.292, E.293, H.296, K.314, E.315, V.319, D.322, N.368, Y.371, Y.376, E.377, Q.817 Ligands: ZN.2, GOL.4 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.114, A:N.254, A:V.289, A:H.292, A:V.319, A:Y.371, A:Y.376, A:Y.376 Hydrogen bonds: A:E.116, A:G.256, A:A.257, A:E.315, A:Y.376 pi-Stacking: A:H.292

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.292, H.296, E.315, Y.376 Ligands: 37B.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.292, A:H.296, A:E.315, A:E.315

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.195, F.196, T.197, K.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.197, A:K.226 GOL.4: 8 residues within 4Å: Chain A: M.255, Y.371, T.372, M.373, Y.376, E.377, R.821 Ligands: 37B.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.377

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.5: 8 residues within 4Å: Chain A: T.198, R.202, N.203, V.204, Y.240, D.241, L.242, D.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.240 Water bridges: A:T.198 IMD.6: 6 residues within 4Å: Chain A: D.21, L.22, H.23, K.34, S.35, R.36 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.36

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

SO4.7: 4 residues within 4Å: Chain A: R.635, L.639, R.687, R.754 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.635, A:R.687 Salt bridges: A:R.635, A:R.754 SO4.8: 1 residues within 4Å: Chain A: D.243 No protein-ligand interaction detected (PLIP) SO4.9: 2 residues within 4Å: Chain A: N.227, R.329 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.227, A:N.227, A:N.227, A:R.329 Salt bridges: A:R.329 SO4.10: 2 residues within 4Å: Chain A: L.401, R.405 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.405 Salt bridges: A:R.405 SO4.11: 3 residues within 4Å: Chain A: T.564, R.567, R.568 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.567, A:R.567, A:R.568, A:R.568, A:R.568 Salt bridges: A:R.567, A:R.568 SO4.12: 3 residues within 4Å: Chain A: N.830, K.837, K.841 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.830, A:N.830, A:K.841, A:K.841 Salt bridges: A:K.837, A:K.841 SO4.13: 2 residues within 4Å: Chain A: A.330, S.331 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.331 Water bridges: A:R.332

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

2014-10-01

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N