SMTL ID : 7cty.1

Wild type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS), fragment 263, NADP+, dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 33 residues within 4Å: Chain A: C.15, A.16, C.17, L.40, G.41, N.42, G.44, V.45, L.46, W.48, G.105, R.106, T.107, S.108, S.111, L.127, S.128, R.129, T.130, L.131, N.144, K.145, V.146, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: GF3.2 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:L.40 Hydrogen bonds: A:A.16, A:L.40, A:N.42, A:G.44, A:G.44, A:R.106, A:T.107, A:T.107, A:S.108, A:S.128, A:R.129, A:R.129, A:R.129, A:T.130, A:G.165, A:G.166, A:S.167, A:V.168, A:V.169, A:E.172, A:E.172 Water bridges: A:S.111 Salt bridges: A:R.106 pi-Cation interactions: A:R.129

2 x GF3: spiro[1H-2-benzofuran-3,4'-piperidine](Non-covalent)

GF3.2: 12 residues within 4Å: Chain A: A.16, L.46, W.48, D.54, M.55, F.58, M.104, S.108, S.111, I.112, I.164 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.46, A:F.58, A:I.112, A:I.164 Hydrogen bonds: A:D.54 GF3.5: 10 residues within 4Å: Chain B: A.16, L.46, W.48, D.54, M.55, F.58, S.108, S.111, I.112, I.164 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.58, B:I.112, B:I.164 Hydrogen bonds: B:D.54

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

PO4.3: 7 residues within 4Å: Chain A: R.345, L.487, C.490, R.510, S.511 Chain B: R.470, R.471 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.345, A:S.511, B:R.470 Salt bridges: A:R.510, B:R.470, B:R.471 PO4.4: 6 residues within 4Å: Chain A: R.470, R.471 Chain B: R.345, C.490, R.510, S.511 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.511 Salt bridges: B:R.510, A:R.470, A:R.471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hoarau, M. et al., Discovery of new non-pyrimidine scaffolds as Plasmodium falciparum DHFR inhibitors by fragment-based screening. J Enzyme Inhib Med Chem (2021)

Release Date

2021-03-31

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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