SMTL ID : 8wgm.1

Quadruple mutant Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S, N51I+C59R+S108N+I164L) complexed with LA1, NADPH and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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, N.108, S.111, L.127, S.128, R.129, T.130, N.144, K.145, V.146, L.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: WCQ.3 24 PLIP interactions: 24 interactions with chain A 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:N.108, A:S.111, A:R.129, A:T.130, A:G.166, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:R.129, A:R.129, A:R.129, A:R.129, A:K.176 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.4: 29 residues within 4Å: Chain B: C.15, A.16, L.40, G.41, G.44, V.45, L.46, W.48, G.105, R.106, T.107, N.108, S.111, L.127, S.128, R.129, T.130, N.144, K.145, L.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: WCQ.6 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:L.40 Hydrogen bonds: B:A.16, B:A.16, B:N.42, B:R.106, B:R.106, B:T.107, B:T.107, B:N.108, B:S.111, B:S.111, B:R.129, B:T.130, B:T.130, B:G.166, B:S.167, B:V.168, B:V.169, B:Y.170, B:E.172 Water bridges: B:N.42, B:G.44 Salt bridges: B:R.106

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE

UMP.2: 14 residues within 4Å: Chain A: R.345, 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 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.513 Hydrogen bonds: A:Q.509, A:S.511, A:S.511, A:D.513, A:N.521, A:N.521, A:H.551 Salt bridges: A:R.345, A:R.510, B:R.470, B:R.471 Water bridges: B:R.471 UMP.5: 14 residues within 4Å: Chain A: R.470, R.471 Chain B: R.345, C.490, H.491, Q.509, R.510, S.511, C.512, D.513, G.517, N.521, H.551, Y.553 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:D.513 Hydrogen bonds: B:Q.509, B:S.511, B:S.511, B:D.513, B:N.521, B:N.521, B:H.551, B:Y.553 Salt bridges: B:R.345, B:R.510, A:R.470, A:R.471 Water bridges: A:R.470, A:R.471

2 x WCQ: (3~{E})-3-[[2-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxypropoxy]phenyl]methylidene]oxolan-2-one

WCQ.3: 17 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, D.54, M.55, F.58, N.108, S.111, I.112, P.113, F.116, L.119, L.164, Y.170, T.185 Ligands: NDP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.46, A:I.112, A:F.116 Hydrogen bonds: A:I.14, A:Y.170, A:T.185, A:T.185 Salt bridges: A:D.54 pi-Stacking: A:F.58 WCQ.6: 16 residues within 4Å: Chain B: I.14, C.15, A.16, L.46, D.54, M.55, F.58, N.108, S.111, I.112, P.113, F.116, L.164, Y.170, T.185 Ligands: NDP.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.46, B:F.116 Hydrogen bonds: B:Y.170, B:T.185, B:T.185 Salt bridges: B:D.54 pi-Stacking: B:F.58

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Decharuangsilp, S. et al., Flexible 2,4-diaminopyrimidine bearing a butyrolactone as Plasmodium falciparum dihydrofolate reductase inhibitors. Bioorg.Chem. (2024)

Release Date

2024-09-11

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional dihydrofolate reductase-thymidylate synthase