SMTL ID : 4kya.4 (3 other biounits)

Crystal structure of non-classical TS inhibitor 3 in complex with Toxoplasma gondii TS-DHFR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.26 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 15 residues within 4Å: Chain A: R.300, L.442, C.445, H.446, Q.465, R.466, S.467, C.468, D.469, N.477, H.507, Y.509 Chain B: R.425, R.426 Ligands: 1UG.2 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Salt bridges: B:R.425, B:R.426, A:R.300, A:R.466 Hydrogen bonds: A:Q.465, A:S.467, A:D.469, A:N.477, A:N.477, A:H.507, A:Y.509 UMP.5: 14 residues within 4Å: Chain A: R.425, R.426 Chain B: C.445, H.446, Q.465, R.466, S.467, C.468, D.469, G.473, N.477, H.507, Y.509 Ligands: 1UG.6 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.465, B:S.467, B:D.469, B:N.477, B:N.477, B:H.507 Salt bridges: B:R.466, A:R.425, A:R.426

2 x 1UG: 2-Amino-5-(1-naphthylsulfanyl)-3,9-dihydro-4H-pyrimido[4,5-b]indol-4-one(Non-covalent)

1UG.2: 10 residues within 4Å: Chain A: I.358, W.359, N.362, D.469, L.472, F.476, Y.509, M.564, A.565 Ligands: UMP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.358, A:I.358, A:L.472, A:L.472, A:M.564 Hydrogen bonds: A:N.362, A:D.469, A:Y.509, A:A.565, A:A.565 Salt bridges: A:D.469 pi-Stacking: A:W.359, A:W.359, A:F.476 1UG.6: 11 residues within 4Å: Chain B: I.358, W.359, N.362, D.469, L.472, G.473, F.476, Y.509, M.564, A.565 Ligands: UMP.5 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.358, B:I.358, B:I.358, B:L.472, B:F.476, B:F.476 Hydrogen bonds: B:N.362, B:A.565 Salt bridges: B:D.469 pi-Stacking: B:W.359, B:W.359

2 x FOL: FOLIC ACID(Non-covalent)

FOL.3: 16 residues within 4Å: Chain A: V.8, V.9, A.10, D.31, F.32, K.33, F.35, S.36, T.58, M.62, F.66, L.69, R.72, V.126, T.147 Ligands: NDP.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.32, A:F.35 Hydrogen bonds: A:V.8, A:S.36, A:T.147, A:T.147 Salt bridges: A:D.31, A:R.72 pi-Stacking: A:F.32 FOL.7: 15 residues within 4Å: Chain B: V.8, V.9, A.10, W.25, D.31, F.32, F.35, S.36, M.62, F.66, L.69, R.72, V.126, T.147 Ligands: NDP.8 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.35, B:F.66 Hydrogen bonds: B:V.8, B:F.32, B:T.147, B:T.147 Salt bridges: B:D.31, B:R.72 pi-Stacking: B:F.32

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.4: 29 residues within 4Å: Chain A: V.9, A.10, I.17, G.18, I.19, N.21, G.22, L.23, W.25, G.55, R.56, K.57, T.58, S.61, V.77, S.78, S.79, S.80, A.103, V.126, G.127, G.128, A.129, G.130, L.131, Y.132, A.134, V.157 Ligands: FOL.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:T.58 Hydrogen bonds: A:A.10, A:I.17, A:I.19, A:G.55, A:R.56, A:R.56, A:K.57, A:T.58, A:T.58, A:S.61, A:S.61, A:S.79, A:S.79, A:S.80, A:G.127, A:G.128, A:A.129, A:G.130, A:G.130 Salt bridges: A:R.56 NDP.8: 24 residues within 4Å: Chain B: V.9, A.10, I.17, G.18, I.19, N.21, G.22, W.25, G.55, R.56, K.57, T.58, S.61, V.77, S.78, S.79, G.128, A.129, G.130, L.131, Y.132, A.134, V.157 Ligands: FOL.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:T.58 Hydrogen bonds: B:A.10, B:I.17, B:I.19, B:G.22, B:R.56, B:K.57, B:T.58, B:T.58, B:S.61, B:S.61, B:S.79, B:S.80, B:G.128, B:A.129, B:G.130 Salt bridges: B:R.56, B:K.57, B:K.57

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zaware, N. et al., Discovery of potent and selective inhibitors of Toxoplasma gondii thymidylate synthase for opportunistic infections. ACS Med Chem Lett (2013)

Release Date

2014-08-06

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

Bifunctional dihydrofolate reductase-thymidylate synthase

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