SMTL ID : 3ijz.1

Lactobacillus casei Thymidylate Synthase ternary complex with dUMP and Pthalimidic derivative 15C

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

2 x 15C: 2-(4-acetylphenyl)-4-methyl-1H-isoindole-1,3(2H)-dione(Non-covalent)

15C.1: 7 residues within 4Å: Chain A: E.60, I.81, W.82, W.85, L.195, G.225 Ligands: UMP.2 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.81, A:I.81, A:W.82, A:W.85 pi-Stacking: A:W.82 Water bridges: B:R.179 15C.3: 7 residues within 4Å: Chain B: E.60, I.81, W.82, W.85, L.195, G.225 Ligands: UMP.4 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.81, B:I.81, B:W.82, B:W.85 pi-Stacking: B:W.82 Water bridges: A:R.179

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.2: 14 residues within 4Å: Chain A: C.198, H.199, Q.217, R.218, S.219, A.220, D.221, G.225, N.229, H.259, Y.261 Chain B: R.178, R.179 Ligands: 15C.1 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:Q.217, A:S.219, A:D.221, A:N.229, A:N.229, A:H.259 Water bridges: A:D.221, B:R.178, B:R.179, B:R.179 Salt bridges: A:R.218, B:R.178, B:R.179 UMP.4: 14 residues within 4Å: Chain A: R.178, R.179 Chain B: C.198, H.199, Q.217, R.218, S.219, A.220, D.221, G.225, N.229, H.259, Y.261 Ligands: 15C.3 14 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:Q.217, B:S.219, B:D.221, B:N.229, B:N.229, B:H.259, B:Y.261 Water bridges: B:Y.146, A:R.178, A:R.179, A:R.179 Salt bridges: B:R.218, A:R.178, A:R.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mangani, S. et al., Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening. J.Med.Chem. (2011)

Release Date

2010-08-11

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate synthase

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