SMTL ID : 8yq9.1

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB6, NADPH and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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, 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: 01.2 23 PLIP interactions: 23 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: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 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.5: 29 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, N.108, S.111, 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 Ligands: 01.6 23 PLIP interactions: 23 interactions with chain B Hydrogen bonds: B:A.16, B:A.16, B:G.44, B:G.44, B:G.105, B:G.105, B:R.106, B:T.107, B:T.107, B:N.108, B:S.111, B:R.129, 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 Salt bridges: B:R.106 pi-Cation interactions: B:R.129

2 x 01: 4-[4-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxypropoxy]phenyl]benzoic acid

01.2: 16 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, C.50, D.54, M.55, F.58, N.108, I.112, P.113, F.116, L.164, Y.170, T.185 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.46, A:I.112, A:P.113, A:F.116 Hydrogen bonds: A:I.14, A:C.15, A:Y.170, A:T.185 Salt bridges: A:D.54 pi-Stacking: A:F.58 01.6: 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.5 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.46, B:F.116 Hydrogen bonds: B:I.14, B:Y.170, B:T.185, B:T.185 Salt bridges: B:D.54

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

UMP.3: 13 residues within 4Å: Chain A: R.345, C.490, H.491, Q.509, R.510, S.511, 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.470 UMP.8: 13 residues within 4Å: Chain A: R.470, R.471 Chain B: R.345, C.490, H.491, Q.509, R.510, S.511, D.513, G.517, N.521, H.551, Y.553 14 PLIP interactions: 11 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 Water bridges: B:R.345, A:R.470 Salt bridges: B:R.345, B:R.510, A:R.470, A:R.471

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Q.455, N.458, L.462, R.471 Chain B: V.479 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.458, A:R.471 GOL.7: 6 residues within 4Å: Chain A: V.479 Chain B: V.453, Q.455, N.458, L.462, R.471 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

Decharuangsilp, S. et al., Novel flexible biphenyl Pf DHFR inhibitors with improved antimalarial activity. Rsc Med 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

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