SMTL ID : 3bz0.1

Lactobacillus Casei Thymidylate Synthase Ternary Complex with DUMP and the Phtalimidic Derivative C00

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 15 residues within 4Å: Chain A: R.23, 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: C00.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.221 Hydrogen bonds: A:Q.217, A:S.219, A:D.221, A:N.229, A:N.229, A:H.259 Salt bridges: A:R.23, A:R.218, B:R.178, B:R.179 UMP.3: 15 residues within 4Å: Chain A: R.178, R.179 Chain B: R.23, C.198, H.199, Q.217, R.218, S.219, A.220, D.221, G.225, N.229, H.259, Y.261 Ligands: C00.4 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:D.221 Hydrogen bonds: B:Q.217, B:S.219, B:D.221, B:N.229, B:N.229, B:H.259, B:Y.261 Salt bridges: B:R.23, B:R.218, A:R.178, A:R.179

2 x C00: 2-(4-hydroxybiphenyl-3-yl)-4-methyl-1H-isoindole-1,3(2H)-dione(Non-covalent)

C00.2: 8 residues within 4Å: Chain A: I.81, W.82, E.84, W.85, L.195, L.224, F.228 Ligands: UMP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.81, A:W.85, A:F.228 Hydrogen bonds: A:W.85 pi-Stacking: A:W.82, A:F.228 C00.4: 8 residues within 4Å: Chain B: I.81, W.82, E.84, W.85, L.195, L.224, F.228 Ligands: UMP.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:I.81, B:W.85, B:F.228 Hydrogen bonds: B:E.84, B:W.85 pi-Stacking: B:W.82, B:F.228

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

2009-01-20

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate synthase

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