SMTL ID : 7ctz.1

Wild-type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with fragment 148, NADPH, and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 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: GF6.3 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:L.40 Hydrogen bonds: A:A.16, A:L.40, A:N.42, A:G.44, A:V.45, A:G.105, 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:T.130, A:G.166, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:S.111 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, I.143, N.144, K.145, V.146, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.16, B:L.40, B:N.42, B:G.44, B:G.105, B:R.106, B:T.107, B:T.107, B:S.108, B:S.111, B:R.129, B:T.130, B:G.165, B:S.167, B:V.168, B:V.169, B:E.172 Salt bridges: B:R.106 pi-Cation interactions: B:R.129, B:R.129

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

UMP.2: 15 residues within 4Å: Chain A: R.345, L.487, C.490, H.491, Q.509, R.510, S.511, C.512, D.513, G.517, N.521, H.551, Y.553 Chain B: R.470, R.471 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Salt bridges: B:R.470, B:R.471, A:R.345, A:R.510 Hydrogen bonds: A:H.491, A:Q.509, A:S.511, A:S.511, A:D.513, A:N.521, A:N.521, A:H.551 UMP.5: 16 residues within 4Å: Chain A: R.470, R.471 Chain B: R.345, L.487, C.490, H.491, Q.509, R.510, S.511, C.512, D.513, G.517, V.518, N.521, H.551, Y.553 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.509, B:S.511, B:D.513, B:N.521, B:N.521, B:H.551, B:Y.553 Water bridges: B:D.513, B:D.513 Salt bridges: B:R.345, B:R.510, A:R.470, A:R.471

1 x GF6: 1-[3-(trifluoromethyl)phenyl]urea(Non-covalent)

GF6.3: 14 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, W.48, D.54, M.55, F.58, S.108, I.112, I.164, Y.170, T.185 Ligands: NDP.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.46, A:F.58 Hydrogen bonds: A:I.164 Water bridges: A:S.111 Halogen bonds: A:D.54

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

2022-02-23

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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