SMTL ID : 4dph.1

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with P65 and NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

2 x P65: 2,4-diamino-6-methyl-5-[3-(2,4,5-trichlorophenoxy)propyloxy]pyrimidine(Non-covalent)

P65.1: 16 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.164, Y.170, T.185 Ligands: NDP.2 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 P65.7: 16 residues within 4Å: Chain B: I.14, C.15, A.16, V.45, L.46, D.54, M.55, F.58, N.108, S.111, I.112, P.113, L.164, Y.170, T.185 Ligands: NDP.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.14, B:C.15, B:T.185 Water bridges: B:T.185 Salt bridges: B:D.54 pi-Stacking: B:F.58

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

NDP.2: 29 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, V.146, L.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: P65.1 21 PLIP interactions: 21 interactions with chain A 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:R.129, A:T.130, A:V.146, A:G.165, A:S.167, A:V.168, A:V.169, A:E.172 Water bridges: A:R.129, A:R.129 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NDP.8: 28 residues within 4Å: Chain B: C.15, A.16, L.40, 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: P65.7 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.40 Hydrogen bonds: B:A.16, B:L.40, 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:S.167, B:V.168, B:V.169, B:Y.170, B:E.172 Salt bridges: B:R.106, B:R.129 pi-Cation interactions: B:R.129, B:R.129

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: R.510, S.511 Chain B: R.470, R.471 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.511, A:S.511 Salt bridges: A:R.510, B:R.471 PO4.9: 5 residues within 4Å: Chain A: R.470, R.471 Chain B: R.345, R.510, S.511 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Salt bridges: A:R.470, A:R.471, B:R.345, B:R.510 Hydrogen bonds: B:S.511, B:S.511

4 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.4: 1 residues within 4Å: Chain A: Y.445 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.445, A:Y.445 BME.5: 3 residues within 4Å: Chain A: Q.99, L.119, R.122 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.99 BME.6: 3 residues within 4Å: Chain A: I.562, N.565, R.566 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.566 Water bridges: A:H.599 BME.10: 6 residues within 4Å: Chain B: F.375, L.376, R.377, G.378, I.379, F.520 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.376, B:G.378, B:I.379

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yuthavong, Y. et al., Malarial dihydrofolate reductase as a paradigm for drug development against a resistance-compromised target. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-11-14

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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