SMTL ID : 3bnz.1

Crystal structure of Thymidylate Synthase ternary complex with dUMP and 8A inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: F.73, H.77, D.295, M.296, K.297 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.295, A:M.296 Salt bridges: A:H.77, A:K.297 PO4.4: 5 residues within 4Å: Chain B: F.73, H.77, D.295, M.296, K.297 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.295, B:D.295, B:M.296 Salt bridges: B:H.77, B:K.297

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

UMP.2: 16 residues within 4Å: Chain A: R.23, L.195, 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: C16.3 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Water bridges: B:R.178 Salt bridges: B:R.178, B:R.179, A:R.23, A:R.218 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 UMP.5: 16 residues within 4Å: Chain A: R.178, R.179 Chain B: R.23, L.195, C.198, H.199, Q.217, R.218, S.219, A.220, D.221, G.225, N.229, H.259, Y.261 Ligands: C16.6 13 PLIP interactions: 3 interactions with chain A, 10 interactions with chain B Water bridges: A:R.178 Salt bridges: A:R.178, A:R.179, B:R.23, B:R.218 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

2 x C16: 4-(4-methyl-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile(Non-covalent)

C16.3: 8 residues within 4Å: Chain A: E.60, I.81, E.84, L.224, G.225, F.228, N.229 Ligands: UMP.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.81, A:F.228, A:F.228 C16.6: 8 residues within 4Å: Chain B: E.60, I.81, E.84, L.224, G.225, F.228, N.229 Ligands: UMP.5 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.81, B:F.228, 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

2008-12-16

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate synthase

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