SMTL ID : 4bcc.1

PROLYL OLIGOPEPTIDASE FROM PORCINE BRAIN WITH A COVALENTLY BOUND P2- substituted N-acyl-prolylpyrrolidine inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x JKT: tert-butyl N-[[1-[(3S,5S)-5-[(2S)-2-[azanyl(oxidanyl)methyl]pyrrolidin-1-yl]carbonyl-1-(4-phenylbutanoyl)pyrrolidin-3-yl]-1,2,3-triazol-4-yl]methyl]carbamate(Covalent)

JKT.1: 20 residues within 4Å: Chain A: F.173, M.235, R.252, G.254, C.255, Y.471, Y.473, F.476, I.480, S.554, N.555, V.580, I.591, A.594, W.595, Y.599, R.643, V.644, H.680 Ligands: GOL.5 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.173, A:F.173, A:R.252, A:F.476, A:F.476, A:I.480, A:V.580, A:I.591, A:A.594, A:W.595, A:W.595, A:V.644 Hydrogen bonds: A:Y.473, A:Y.473, A:N.555, A:R.643 Water bridges: A:R.643

1 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.2: 4 residues within 4Å: Chain A: K.445, D.446, N.522, N.525 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:D.446 Hydrogen bonds: A:D.446, A:N.525 Water bridges: A:K.445, A:R.505, A:D.528

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: E.323, W.326, V.328 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.323, A:S.324 GOL.4: 7 residues within 4Å: Chain A: A.226, E.227, F.228, W.262, I.276, W.279, K.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.227, A:K.281, A:K.281 GOL.5: 5 residues within 4Å: Chain A: G.553, S.554, V.578, H.680 Ligands: JKT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.553, A:H.680 Water bridges: A:Q.577 GOL.6: 10 residues within 4Å: Chain A: P.568, D.569, F.571, G.572, D.627, I.628, Q.629, Y.630, P.631, N.668 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.569, A:F.571, A:D.627, A:Q.629, A:Y.630, A:N.668 Water bridges: A:Q.629, A:Q.629 GOL.7: 3 residues within 4Å: Chain A: E.239, D.291, Y.292 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.291 Water bridges: A:E.239, A:E.239, A:D.242, A:S.250 GOL.8: 4 residues within 4Å: Chain A: W.340, V.341, A.342, Y.385 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.341, A:V.341, A:G.387 GOL.9: 6 residues within 4Å: Chain A: D.8, V.9, W.30, Q.38, A.41, F.42 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.38 Water bridges: A:D.8, A:Y.10 GOL.10: 6 residues within 4Å: Chain A: V.258, E.287, G.288, N.305, E.512, K.516 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.287, A:E.512, A:K.516 Water bridges: A:H.307 GOL.11: 7 residues within 4Å: Chain A: R.170, Y.190, P.191, Q.193, T.204, N.205, L.206 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.170, A:N.205, A:L.206 Water bridges: A:Q.193, A:T.204

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Der Veken, P. et al., P2-Substituted N-Acylprolylpyrrolidine Inhibitors of Prolyl Oligopeptidase: Biochemical Evaluation, Binding Mode Determination, and Assessment in a Cellular Model of Synucleinopathy. J.Med.Chem. (2012)

Release Date

2013-03-13

Peptides

PROLYL ENDOPEPTIDASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

PROLYL ENDOPEPTIDASE

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