SMTL ID : 5t0l.1

Crystal structure of Toxoplasma gondii TS-DHFR complexed with NADPH, dUMP, PDDF and 5-(4-(3,4-dichlorophenyl)piperazin-1-yl)pyrimidine-2,4-diamine (TRC-15)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 16 residues within 4Å: Chain A: R.300, L.442, C.445, H.446, Q.465, R.466, S.467, C.468, D.469, G.473, N.477, H.507, Y.509 Chain B: R.425, R.426 Ligands: CB3.3 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:D.469 Hydrogen bonds: A:Q.465, A:S.467, A:D.469, A:N.477, A:N.477, A:H.507, A:Y.509 Salt bridges: A:R.300, A:R.466, B:R.425, B:R.426 UMP.5: 16 residues within 4Å: Chain A: R.425, R.426 Chain B: R.300, Y.385, L.442, C.445, H.446, Q.465, R.466, S.467, D.469, G.473, N.477, H.507, Y.509 Ligands: CB3.7 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:D.469 Hydrogen bonds: B:Q.465, B:S.467, B:S.467, B:D.469, B:N.477, B:N.477, B:H.507, A:R.425, A:R.425 Salt bridges: B:R.300, B:R.466, A:R.425, A:R.426

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

NDP.2: 26 residues within 4Å: Chain A: V.9, A.10, I.17, G.18, 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 Ligands: 73X.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.58 Hydrogen bonds: A:A.10, A:I.17, A:N.21, A:G.55, A:R.56, A:R.56, A:K.57, A:T.58, A:S.61, A:S.79, A:S.80, A:G.128, A:A.129, A:G.130 Salt bridges: A:R.56 NDP.6: 26 residues within 4Å: Chain B: 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, V.77, S.78, S.79, S.80, A.103, V.126, G.127, G.128, A.129, G.130, Y.132, V.157 Ligands: 73X.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.58 Hydrogen bonds: B:A.10, B:A.10, B:I.19, B:N.21, B:R.56, B:R.56, B:K.57, B:T.58, B:S.79, B:S.80, B:L.81, B:G.128, B:A.129, B:G.130 Salt bridges: B:R.56

2 x CB3: 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID(Non-covalent)

CB3.3: 17 residues within 4Å: Chain A: K.327, R.328, V.329, F.330, I.358, W.359, N.362, D.469, L.472, G.473, F.476, N.477, Y.509, R.559, M.564, A.565 Ligands: UMP.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.330, A:I.358, A:I.358, A:W.359, A:F.476, A:F.476, A:F.476 Hydrogen bonds: A:R.328, A:D.469, A:F.476, A:Y.509, A:A.565, A:A.565, A:A.565 Salt bridges: A:K.327, A:D.469, A:R.559 pi-Stacking: A:F.476 CB3.7: 18 residues within 4Å: Chain B: K.327, R.328, V.329, F.330, E.337, I.358, W.359, N.362, D.469, L.472, G.473, F.476, N.477, Y.509, R.559, M.564, A.565 Ligands: UMP.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.330, B:I.358, B:I.358, B:W.359, B:F.476, B:F.476 Hydrogen bonds: B:F.330, B:D.469, B:Y.509, B:A.565 Salt bridges: B:K.327, B:D.469, B:R.559 pi-Stacking: B:F.476

2 x 73X: 5-[4-(3,4-dichlorophenyl)piperazin-1-yl]pyrimidine-2,4-diamine(Non-covalent)

73X.4: 14 residues within 4Å: Chain A: V.8, V.9, A.10, D.31, F.32, F.35, S.61, M.62, P.63, F.66, V.126, Y.132, T.147 Ligands: NDP.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.8, A:Y.132, A:Y.145, A:T.147 Salt bridges: A:D.31 pi-Stacking: A:F.32 73X.8: 14 residues within 4Å: Chain B: V.8, V.9, A.10, L.23, D.31, F.32, F.35, S.61, M.62, P.63, V.126, Y.132, T.147 Ligands: NDP.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.8, B:V.9, B:Y.132 Salt bridges: B:D.31 pi-Stacking: B:F.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Welsch, M.E. et al., Discovery of Potent and Selective Leads against Toxoplasma gondii Dihydrofolate Reductase via Structure-Based Design. ACS Med Chem Lett (2016)

Release Date

2016-09-28

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional dihydrofolate reductase-thymidylate synthase

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