SMTL ID : 6a2k.1

Crystal structure of wild type Plasmodium falciparum DHFR-TS complexed with BT1, NADPH, and dUMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

homo-dimer

Ligands

2 x 9QO: 5-(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-6-ethylpyrimidine-2,4-diamine(Non-covalent)

9QO.1: 14 residues within 4Å: Chain A: I.14, C.15, A.16, L.46, D.54, M.55, F.58, S.111, P.113, F.116, I.164, Y.170, T.185 Ligands: NAP.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.46, A:L.46, A:F.58, A:F.58, A:I.164 Hydrogen bonds: A:I.14, A:C.15, A:Y.170, A:T.185 Water bridges: A:L.46, A:K.49 Salt bridges: A:D.54 9QO.4: 15 residues within 4Å: Chain B: I.14, C.15, A.16, L.46, D.54, M.55, F.58, S.111, I.112, P.113, F.116, I.164, Y.170, T.185 Ligands: NAP.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.58, B:I.112, B:I.164 Hydrogen bonds: B:I.14, B:C.15, B:T.185 Salt bridges: B:D.54 pi-Stacking: B:F.58

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 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, S.108, L.127, S.128, R.129, T.130, N.144, K.145, V.146, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: 9QO.1 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:L.40 Hydrogen bonds: A:A.16, A:A.16, A:N.42, A:G.44, A:G.44, A:G.105, A:R.106, A:T.107, A:T.107, A:S.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:N.42, A:R.106, A:R.129, A:R.129, A:R.129, A:V.146 Salt bridges: A:R.106 pi-Cation interactions: A:R.129 NAP.5: 28 residues within 4Å: Chain B: C.15, A.16, L.40, G.41, G.44, V.45, L.46, G.105, R.106, T.107, S.108, L.127, S.128, R.129, T.130, N.144, K.145, V.146, I.164, G.165, G.166, S.167, V.168, V.169, Y.170, E.172, V.195 Ligands: 9QO.4 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:L.40 Hydrogen bonds: B:A.16, B:G.44, B:G.105, B:R.106, B:T.107, B:T.107, B:S.108, B:S.128, B:R.129, B:R.129, B:T.130, B:S.167, B:V.168, B:V.169, B:Y.170, B:Y.170, B:E.172 Water bridges: B:V.146 Salt bridges: B:R.106 pi-Cation interactions: B:R.129

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

UMP.3: 13 residues within 4Å: Chain A: 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 11 PLIP interactions: 8 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.510, B:R.470, B:R.471 Water bridges: B:R.471 UMP.6: 15 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, V.518, N.521, H.551, Y.553 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:D.513 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tarnchompoo, B. et al., Hybrid Inhibitors of Malarial Dihydrofolate Reductase with Dual Binding Modes That Can Forestall Resistance. ACS Med Chem Lett (2018)

Release Date

2019-04-24

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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