SMTL ID : 6pf5.2 (2 other biounits)

Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and 2-(2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)-4-methoxyphenyl)acetic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 15 residues within 4Å: Chain A: R.27, L.169, C.172, H.173, Q.191, R.192, S.193, G.194, D.195, G.199, N.203, H.233, Y.235 Chain B: R.152 Ligands: OED.2 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.191, A:S.193, A:D.195, A:N.203, A:N.203, A:H.233, A:Y.235 Salt bridges: A:R.27, A:R.192, B:R.152 Water bridges: B:R.152 UMP.3: 15 residues within 4Å: Chain A: R.152 Chain B: R.27, L.169, C.172, H.173, Q.191, R.192, S.193, G.194, D.195, G.199, N.203, H.233, Y.235 Ligands: OED.4 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.191, B:S.193, B:D.195, B:N.203, B:N.203, B:H.233 Salt bridges: B:R.27, B:R.192, A:R.152 Water bridges: A:R.152

2 x OED: [2-({4-[(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzene-1-carbonyl}amino)-4-methoxyphenyl]acetic acid(Non-covalent)

OED.2: 12 residues within 4Å: Chain A: R.55, F.57, I.85, W.86, D.195, L.198, G.199, F.202, Y.235, M.288, A.289 Ligands: UMP.1 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.57, A:F.57, A:I.85, A:L.198, A:F.202 Hydrogen bonds: A:D.195, A:Y.235, A:A.289, A:A.289 Water bridges: A:F.57, A:D.195 Salt bridges: A:D.195 pi-Stacking: A:F.202 OED.4: 12 residues within 4Å: Chain B: R.55, F.57, I.85, W.86, D.195, L.198, G.199, F.202, Y.235, M.288, A.289 Ligands: UMP.3 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.57, B:F.57, B:I.85, B:L.198, B:F.202 Hydrogen bonds: B:A.289, B:A.289 Water bridges: B:F.57, B:D.195 Salt bridges: B:D.195 pi-Stacking: B:F.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czyzyk, D.J. et al., Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Eur.J.Med.Chem. (2019)

Release Date

2019-10-02

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Thymidylate synthase

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