SMTL ID : 6zxo.1 (2 other biounits)

Crystal structure of His-tagged human thymidylate synthase (HT-hTS) in complex with FdUMP and Raltitrexed (Tomudex)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x D16: TOMUDEX(Non-covalent)

D16.1: 12 residues within 4Å: Chain A: F.92, I.120, W.121, D.230, L.233, G.234, F.237, N.238, Y.270, M.323, A.324 Ligands: UFP.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.92, A:W.121, A:F.237, A:Y.270 Hydrogen bonds: A:G.234 pi-Stacking: A:F.237 D16.4: 12 residues within 4Å: Chain B: F.92, E.99, I.120, W.121, D.230, L.233, G.234, F.237, Y.270, M.323, A.324 Ligands: UFP.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:W.121, B:F.237, B:Y.270 Hydrogen bonds: B:D.230 Water bridges: B:A.324 Salt bridges: B:K.89, B:K.320 pi-Stacking: B:F.237

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

UFP.2: 16 residues within 4Å: Chain A: R.62, W.121, C.207, H.208, Q.226, R.227, S.228, G.229, D.230, G.234, N.238, H.268, Y.270 Chain B: R.187, R.188 Ligands: D16.1 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.226, A:S.228, A:D.230, A:N.238, A:N.238, A:H.268, A:Y.270 Water bridges: A:R.62 Salt bridges: A:R.62, A:R.227, B:R.187, B:R.188 UFP.5: 17 residues within 4Å: Chain A: R.187, R.188 Chain B: R.62, W.121, L.204, C.207, H.208, Q.226, R.227, S.228, G.229, D.230, G.234, N.238, H.268, Y.270 Ligands: D16.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:D.230 Hydrogen bonds: B:Q.226, B:S.228, B:S.228, B:D.230, B:N.238, B:N.238, B:H.268 Water bridges: B:R.62, A:R.187 Salt bridges: B:R.62, B:R.227, A:R.187, A:R.188

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: Q.48, M.73, Q.74 Chain B: Q.74 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.48, A:Q.74 Water bridges: A:G.72 EDO.6: 5 residues within 4Å: Chain A: V.57 Chain B: R.80, V.216, E.219, D.259 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.80 Water bridges: B:S.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pozzi, C. et al., Structural Bases for the Synergistic Inhibition of Human Thymidylate Synthase and Ovarian Cancer Cell Growth by Drug Combinations. Cancers (Basel) (2021)

Release Date

2021-05-19

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase

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