SMTL ID : 5y4p.1 (1 other biounit)

Crystal structure of Trypanosoma cruzi spermidine synthase in complex with 5-methoxy-2-(5-methyl-4,5-dihydro-1H-imidazol-2-yl)phenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

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

S4M.1: 17 residues within 4Å: Chain A: Q.48, L.67, Q.72, 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 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Q.48, A:H.82, A:I.127, A:D.157, A:D.157, A:G.158 Water bridges: A:G.108 Salt bridges: A:D.106, A:D.176 S4M.3: 20 residues within 4Å: Chain B: Q.48, M.65, 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Q.72, B:V.73 Hydrogen bonds: B:Q.48, B:G.103, B:D.106, B:I.127, B:D.157, B:G.158, B:T.178 Water bridges: B:G.108 Salt bridges: B:D.106, B:D.176

2 x 8QO: 5-methoxy-2-[(5R)-5-methyl-4,5-dihydro-1H-imidazol-2-yl]phenol(Non-covalent)

8QO.2: 10 residues within 4Å: Chain A: E.22, M.32, L.34, W.61, I.71, T.74, D.77, Y.81, T.244 Chain B: Q.30 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.71, A:I.71, A:T.74 Hydrogen bonds: A:E.22 pi-Stacking: A:W.61 8QO.4: 12 residues within 4Å: Chain A: Q.30 Chain B: E.22, M.32, L.34, W.61, I.71, T.74, D.77, Y.81, T.244, Y.245, P.246 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.71, B:I.71, B:T.74, B:Y.245 Hydrogen bonds: B:E.22, B:Y.81 pi-Stacking: B:W.61

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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