SMTL ID : 3t60.1

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-trimer

Ligands

3 x DUA: 2',5'-dideoxy-5'-(tritylamino)uridine(Non-covalent)

DUA.1: 13 residues within 4Å: Chain A: F.46, L.88, N.103, G.106, L.107, I.108, Y.112, I.116, I.117, A.119 Chain B: S.92, S.93, S.95 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:Y.112, A:I.117, A:I.117, A:A.119 Hydrogen bonds: A:N.103, A:I.117, A:I.117 pi-Stacking: A:F.46 DUA.3: 14 residues within 4Å: Chain B: F.46, L.88, N.103, G.106, L.107, I.108, Y.112, I.116, I.117, A.119 Chain C: S.92, S.93, S.95, K.96 14 PLIP interactions: 1 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:K.96, B:F.46, B:F.46, B:F.46, B:Y.112, B:I.117, B:I.117, B:A.119 Hydrogen bonds: B:N.103, B:I.117, B:I.117 Water bridges: B:Y.112, B:A.119 pi-Stacking: B:F.46 DUA.5: 13 residues within 4Å: Chain A: S.92, S.93, S.95 Chain C: F.46, L.88, N.103, G.106, L.107, Y.112, E.115, I.116, I.117, A.119 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.46, C:F.46, C:Y.112, C:I.117, C:I.117, C:A.119 Hydrogen bonds: C:N.103, C:I.117, C:I.117 pi-Stacking: C:F.46

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: R.91, S.92, S.93, Q.138 6 PLIP interactions: 1 interactions with chain C, 5 interactions with chain A Water bridges: C:L.107, A:S.92 Hydrogen bonds: A:S.92, A:S.93, A:S.93, A:Q.138 GOL.4: 4 residues within 4Å: Chain B: R.91, S.92, S.93, Q.138 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:L.107, A:L.107 Hydrogen bonds: B:S.92, B:S.93, B:Q.138 GOL.6: 5 residues within 4Å: Chain B: L.107 Chain C: R.91, S.92, S.93, Q.138 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.93, B:L.107 Water bridges: B:L.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hampton, S.E. et al., Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase. Chemmedchem (2011)

Release Date

2012-08-29

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative