SMTL ID : 6kp7.1

Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with B12154

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 30 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, 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: DQ9.3 20 PLIP interactions: 20 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:N.108, A:R.129, A:T.130, A:G.165, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:V.146 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, 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.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: DQ9.6 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.40 Hydrogen bonds: B:A.16, B:L.40, B:N.42, B:G.44, B:G.44, B:R.106, B:T.107, B:T.107, B:N.108, B:R.129, B:R.129, B:T.130, B:K.145, B:K.145, B:G.165, B:S.167, B:V.168, B:V.169, B:Y.170 Salt bridges: B:R.106

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

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:D.513, A:N.521, A:N.521, A:H.551 Water bridges: A:H.491, B:R.470 Salt bridges: A:R.345, A:R.510, B:R.470, 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 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A 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

2 x DQ9: 2-[3-[3-[2,6-bis(azanyl)-5-(3-chlorophenyl)pyrimidin-4-yl]propoxy]phenoxy]ethanoic acid(Non-covalent)

DQ9.3: 16 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, D.54, M.55, F.58, R.59, N.108, I.112, F.116, L.119, L.164, Y.170, T.185 Ligands: NDP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.46, A:F.58, A:F.58, A:F.58, A:L.119 Hydrogen bonds: A:I.14, A:Y.170, A:T.185, A:T.185 Water bridges: A:R.122, A:R.122, A:R.122 Salt bridges: A:D.54, A:R.59 DQ9.6: 15 residues within 4Å: Chain B: I.14, C.15, A.16, L.46, D.54, M.55, F.58, R.59, N.108, I.112, F.116, L.164, Y.170, T.185 Ligands: NDP.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.46, B:F.58, B:F.58, B:F.58, B:I.112 Hydrogen bonds: B:I.14, B:T.185, B:T.185 Salt bridges: B:D.54, B:R.59

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: W.477 Chain B: V.453, Q.455, N.458, L.462, R.471, L.473 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.458, B:R.471

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saepua, S. et al., 6-Hydrophobic aromatic substituent pyrimethamine analogues as potential antimalarials for pyrimethamine-resistant Plasmodium falciparum. Bioorg.Med.Chem. (2019)

Release Date

2019-12-04

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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