SMTL ID : 4qhp.1

Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe(4-CH2NH2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x 32Q: (2S)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid(Non-covalent)

32Q.1: 27 residues within 4Å: Chain A: M.106, Q.118, E.120, P.121, F.257, N.258, 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, Q.327, N.372, Y.375, Y.380, E.381, Q.821 Ligands: ZN.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Q.118, A:N.258, A:V.293, A:H.296, A:V.323, A:Y.375, A:Y.380, A:Y.380 Hydrogen bonds: A:E.120, A:G.260, A:A.261, A:K.318, A:E.319, A:D.326, A:Y.380 pi-Stacking: A:H.296

1 x 32R: (2R)-2-[4-(aminomethyl)benzyl]-3-[(R)-[(1R)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]propanoic acid(Non-covalent)

32R.2: 14 residues within 4Å: Chain A: K.139, N.159, P.178, F.179, T.202, R.206, N.207, V.208, Y.244, D.245, L.246, D.247, R.306 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.178, A:F.179, A:F.179, A:F.179, A:R.206, A:V.208, A:D.247 Hydrogen bonds: A:N.159, A:N.159 Water bridges: A:R.206

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 7 residues within 4Å: Chain A: D.25, L.26, H.27, K.38, S.39, R.40, T.143 4 PLIP interactions: 4 interactions with chain A Water bridges: A:S.39, A:R.40, A:E.92 pi-Cation interactions: A:R.40

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: Y.199, F.200, T.201, K.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.201, A:K.230 GOL.5: 5 residues within 4Å: Chain A: P.588, K.589, H.590, E.591, K.592 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.589, A:H.590, A:E.591, A:K.592 GOL.6: 4 residues within 4Å: Chain A: A.695, H.696, E.698, T.699 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.695, A:T.699, A:T.699 Water bridges: A:T.699 GOL.7: 2 residues within 4Å: Chain A: R.206 Ligands: 32R.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.206, A:R.206

1 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: H.296, H.300, E.319, Y.380 Ligands: 32Q.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.296, A:H.300, A:E.319, A:E.319

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

SO4.9: 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 SO4.10: 6 residues within 4Å: Chain A: N.658, R.682, R.686, K.703, M.707, I.717 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.658 Water bridges: A:K.703, A:K.703 Salt bridges: A:R.682, A:R.686, A:K.703 SO4.11: 2 residues within 4Å: Chain A: L.405, R.409 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.409 SO4.12: 3 residues within 4Å: Chain A: R.639, L.643, R.758 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.639, A:R.639, A:R.691, A:R.758, A:R.758, A:R.758 Salt bridges: A:R.639, A:R.758 SO4.13: 2 residues within 4Å: Chain A: R.280, K.739 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.739 Salt bridges: A:R.280, A:K.739 SO4.14: 3 residues within 4Å: Chain A: T.568, R.571, R.572 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.541, A:N.541, A:R.571, A:R.572 Salt bridges: A:R.571, A:R.572 SO4.15: 2 residues within 4Å: Chain A: N.231, R.333 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.231, A:N.231, A:N.231, A:R.333 Salt bridges: A:R.333 SO4.16: 2 residues within 4Å: Chain A: A.495, R.502 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.495 Salt bridges: A:R.502 SO4.17: 5 residues within 4Å: Chain A: A.662, Q.667, Y.669, R.682, M.707 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.667, A:Y.669 Water bridges: A:E.665, A:R.682 Salt bridges: A:R.682 SO4.18: 3 residues within 4Å: Chain A: N.834, K.841, K.845 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.834 Water bridges: A:N.834, A:K.845, A:K.845, A:K.845 Salt bridges: A:K.841, A:K.845

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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