SMTL ID : 3epx.1

Crystal structure of Trypanosoma vivax nucleoside hydrolase in complex with the inhibitor (2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidin-3,4-diol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.21, D.26, T.148, D.272 Ligands: IMQ.2 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.21, A:D.26, A:D.26, A:T.148, A:D.272 CA.4: 5 residues within 4Å: Chain B: D.21, D.26, T.148, D.272 Ligands: IMQ.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.21, B:D.26, B:T.148, B:D.272, H2O.16

2 x IMQ: (2R,3R,4S)-2-(hydroxymethyl)-1-(quinolin-8-ylmethyl)pyrrolidine-3,4-diol(Non-covalent)

IMQ.2: 17 residues within 4Å: Chain A: N.23, D.25, D.26, D.51, F.90, W.94, T.148, M.175, N.184, E.195, W.196, N.197, G.265, Y.268, W.271, D.272 Ligands: CA.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:W.94, A:W.271, A:W.271 Hydrogen bonds: A:D.25, A:D.51, A:N.184, A:N.184, A:W.196, A:N.197, A:D.272 Salt bridges: A:D.25, A:D.51 pi-Stacking: A:W.94, A:W.94, A:W.94, A:Y.268 IMQ.5: 17 residues within 4Å: Chain B: N.23, D.25, D.26, D.51, F.90, W.94, T.148, M.175, N.184, E.195, W.196, N.197, D.266, Y.268, W.271, D.272 Ligands: CA.4 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:W.271, B:W.271 Hydrogen bonds: B:D.25, B:N.184, B:N.184, B:E.195, B:W.196, B:N.197, B:D.272 Salt bridges: B:D.25, B:D.51, B:D.272 pi-Stacking: B:W.94, B:W.94, B:W.94, B:Y.268

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: P.322, E.323, A.324, E.325 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.322, A:A.324, A:E.325 Water bridges: A:F.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Versees, W. et al., Crystal structures of T. vivax nucleoside hydrolase in complex with new potent and specific inhibitors. Biochim.Biophys.Acta (2009)

Release Date

2009-03-24

Peptides

IAG-nucleoside hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

IAG-nucleoside hydrolase

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