SMTL ID : 5y4q.1 (1 other biounit)

Crystal structure of Trypanosoma cruzi spermidine synthase in complex with N-(4-methoxyphenyl)quinolin-4-amine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

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

S4M.1: 20 residues within 4Å: Chain A: Q.48, L.67, Q.72, V.73, 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 Ligands: 8OF.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.48, A:H.82, A:G.103, A:I.127, A:D.128, A:D.157, A:D.157, A:G.158 Salt bridges: A:D.106, A:D.176 S4M.3: 21 residues within 4Å: Chain B: Q.48, L.67, Q.72, V.73, 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, A.184, L.187 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.72, B:V.73 Hydrogen bonds: B:Q.48, B:H.82, B:G.103, B:I.127, B:G.158, B:A.184, B:A.184 Water bridges: B:G.108 Salt bridges: B:D.106, B:D.176

2 x 8OF: N-(4-methoxyphenyl)quinolin-4-amine(Non-covalent)

8OF.2: 12 residues within 4Å: Chain A: E.22, M.32, W.61, I.71, Q.72, D.77, Y.81, V.242, T.244, Y.245, P.246 Ligands: S4M.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.71, A:I.71, A:Y.81, A:Y.81, A:V.242, A:Y.245 Hydrogen bonds: A:D.77 Water bridges: A:D.77 pi-Stacking: A:W.61, A:Y.245 8OF.4: 12 residues within 4Å: Chain B: E.22, W.61, I.71, Q.72, T.74, D.77, Y.81, Q.209, V.242, T.244, Y.245, I.250 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.71, B:I.71, B:T.74, B:V.242, B:Y.245, B:I.250 Hydrogen bonds: B:T.244 pi-Stacking: B:W.61, B:Y.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoshino, R. et al., Discovery of a Hidden Trypanosoma cruzi Spermidine Synthase Binding Site and Inhibitors through In Silico, In Vitro , and X-ray Crystallography. Acs Omega (2023)

Release Date

2018-08-08

Peptides

Spermidine synthase, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Spermidine synthase, putative

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