SMTL ID : 5b1s.2 (1 other biounit)

Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 2-(2-fluorophenyl)ethanamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 x S4M: 5'-[(S)-(3-AMINOPROPYL)(METHYL)-LAMBDA~4~-SULFANYL]-5'-DEOXYADENOSINE(Non-covalent)

S4M.1: 25 residues within 4Å: Chain A: Q.48, L.67, Q.72, V.73, Y.81, H.82, G.103, G.104, D.106, V.125, D.126, I.127, D.128, V.131, G.156, D.157, G.158, D.176, T.177, T.178, P.183, A.184, L.187, Y.245 Ligands: BSX.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.72 Hydrogen bonds: A:Q.48, A:D.106, A:I.127, A:G.158, A:T.178, A:P.183 Water bridges: A:G.108 Salt bridges: A:D.106, A:D.176 S4M.3: 25 residues within 4Å: Chain B: Q.48, L.67, Q.72, V.73, Y.81, H.82, G.103, G.104, D.106, V.125, D.126, I.127, D.128, V.131, G.156, D.157, G.158, D.176, T.177, T.178, P.183, A.184, L.187, Y.245 Ligands: BSX.4 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.72 Hydrogen bonds: B:Q.48, B:H.82, B:G.103, B:I.127, B:D.157, B:G.158, B:T.178, B:P.183 Water bridges: B:G.108 Salt bridges: B:D.106, B:D.176

2 x BSX: 2-(2-fluorophenyl)ethanamine(Non-covalent)

BSX.2: 12 residues within 4Å: Chain A: W.27, Q.72, Y.81, D.176, T.177, T.178, D.179, Q.209, Y.245, P.246, I.250 Ligands: S4M.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.81, A:Y.81, A:Q.209 Water bridges: A:D.179 pi-Stacking: A:Y.245 BSX.4: 13 residues within 4Å: Chain B: W.27, I.71, Q.72, Y.81, D.176, T.177, T.178, D.179, Q.209, Y.245, P.246, I.250 Ligands: S4M.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.81, B:Y.81, B:Q.209, B:Y.245, B:I.250 Water bridges: B:D.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshino, R. et al., In silico, in vitro, X-ray crystallography, and integrated strategies for discovering spermidine synthase inhibitors for Chagas disease. Sci Rep (2017)

Release Date

2016-12-21

Peptides

Spermidine synthase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Spermidine synthase, putative

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