SMTL ID : 6lhj.1

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with C452 (compound 16) and NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x EA6: 1-[3-(2-chloranyl-4-fluoranyl-phenoxy)propoxy]-6,6-dimethyl-1,3,5-triazine-2,4-diamine(Non-covalent)

EA6.1: 16 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, D.54, M.55, F.58, N.108, I.112, P.113, F.116, L.119, L.164, Y.170, T.185 Ligands: NDP.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.46, A:L.46, A:F.58 Hydrogen bonds: A:I.14, A:C.15, A:Y.170, A:T.185 Salt bridges: A:D.54 pi-Stacking: A:F.116 EA6.5: 15 residues within 4Å: Chain B: I.14, C.15, A.16, L.46, D.54, M.55, F.58, N.108, I.112, P.113, F.116, L.164, Y.170, T.185 Ligands: NDP.6 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.16, B:L.46, B:F.58, B:F.116 Hydrogen bonds: B:I.14, B:C.15, B:T.185 Salt bridges: B:D.54, B:D.54

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

NDP.2: 30 residues within 4Å: Chain A: C.15, A.16, L.40, G.41, N.42, G.44, V.45, L.46, 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: EA6.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.40, A:L.46 Hydrogen bonds: A:A.16, A:L.40, A:N.42, A:G.44, A:R.106, A:T.107, A:T.107, A:N.108, A:S.111, A:S.128, A:R.129, A:R.129, A:T.130, A:V.146, A:G.165, A:G.166, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:G.44, A:T.107 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.6: 28 residues within 4Å: Chain B: C.15, A.16, L.40, G.41, N.42, G.44, V.45, L.46, G.105, R.106, T.107, N.108, L.127, S.128, R.129, T.130, N.144, K.145, V.146, L.164, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: EA6.5 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:A.16, B:L.40, B:N.42, B:G.44, B:G.44, B:G.105, B:R.106, B:T.107, B:T.107, B:N.108, B:S.111, B:S.128, 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:G.41, B:L.46 Salt bridges: B:R.106, B:R.129 pi-Cation interactions: B:R.129, B:R.129

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

UMP.3: 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 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:D.513 Hydrogen bonds: A:Q.509, 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.470 UMP.7: 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 12 PLIP interactions: 9 interactions with chain B, 3 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 Salt bridges: B:R.345, B:R.510, A:R.470, A:R.471 Water bridges: A:R.470

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: V.453, Q.455, N.458, I.459, L.462, R.471, L.473 Chain B: W.477, V.479, L.482 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.458 Water bridges: A:Q.455

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kamchonwongpaisan, S. et al., Flexible diaminodihydrotriazine inhibitors of Plasmodium falciparum dihydrofolate reductase: Binding strengths, modes of binding and their antimalarial activities. Eur.J.Med.Chem. (2020)

Release Date

2020-11-11

Peptides

Bifunctional dihydrofolate reductase-thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional dihydrofolate reductase-thymidylate synthase

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