SMTL ID : 3t64.2 (1 other biounit)

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-trimer

Ligands

3 x DU3: 2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine(Non-covalent)

DU3.1: 15 residues within 4Å: Chain A: F.46, L.88, N.103, G.106, L.107, I.108, Y.112, E.115, I.116, I.117, A.119 Chain B: S.92, S.95, K.96 Ligands: SO4.4 13 PLIP interactions: 1 interactions with chain B, 12 interactions with chain A Water bridges: B:S.92, A:L.107 Hydrophobic interactions: A:F.46, A:F.46, A:I.108, 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 DU3.3: 14 residues within 4Å: Chain B: F.46, L.88, N.103, G.106, L.107, I.108, Y.112, E.115, I.116, I.117, A.119 Chain C: S.92, S.95 Ligands: SO4.6 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.46, B:F.46, B:I.108, 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: C:S.92 DU3.5: 13 residues within 4Å: Chain A: S.92, S.95 Chain C: F.46, L.88, N.103, G.106, L.107, Y.112, E.115, I.116, I.117, A.119 Ligands: SO4.2 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: 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 Water bridges: C:L.107, C:D.109, C:Y.112, C:Y.112

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: R.91, S.92, Q.138 Chain C: L.107 Ligands: DU3.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.92, A:Q.138 Water bridges: A:S.93, A:S.93, C:L.107 SO4.4: 6 residues within 4Å: Chain A: L.107, D.109 Chain B: R.91, S.92, Q.138 Ligands: DU3.1 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.92, B:Q.138 Water bridges: B:S.92, B:S.92, B:S.93, B:S.93, A:L.107 SO4.6: 5 residues within 4Å: Chain B: D.109 Chain C: R.91, S.92, Q.138 Ligands: DU3.3 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.92, C:S.92, C:Q.138 Water bridges: C:S.92, C:S.92, C:S.93 SO4.7: 4 residues within 4Å: Chain C: G.111, Y.112, R.113, R.160 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.111, C:R.113, C:G.114 Salt bridges: C:R.113, C:R.160

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

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