SMTL ID : 7ctw.1

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with fragment 820, NADPH, dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 31 residues within 4Å: Chain A: C.15, A.16, 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, 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: GEX.2 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:A.16, A:L.40, A:N.42, A:G.44, A:G.44, A:G.105, A:R.106, A:T.107, A:T.107, A:S.108, A:S.111, A:R.129, A:R.129, A:R.129, A:R.129, A:T.130, A:T.130, A:G.165, A:G.166, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:S.111, A:V.146, A:Y.170 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.4: 31 residues within 4Å: Chain B: C.15, A.16, 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 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.164 Hydrogen bonds: B:A.16, B:L.40, B:G.44, B:G.105, B:T.107, B:T.107, B:S.108, B:S.111, B:R.129, B:R.129, B:R.129, B:T.130, B:S.167, B:V.168, B:V.169, B:E.172 Salt bridges: B:R.106

1 x GEX: 1-(2-methylsulfanylphenyl)piperazine(Non-covalent)

GEX.2: 13 residues within 4Å: Chain A: A.16, L.46, W.48, D.54, M.55, F.58, S.108, I.112, P.113, F.116, L.119, I.164 Ligands: NDP.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.112, A:I.112 Hydrogen bonds: A:D.54

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

PO4.3: 5 residues within 4Å: Chain A: R.345, R.510, S.511 Chain B: R.470, R.471 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.511, B:R.470 Salt bridges: A:R.345, A:R.510, B: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

2021-04-28

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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