SMTL ID : 3t6y.1

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

1 x ALA- HIS- ALA: peptide ALA-HIS-ALA(Non-covalent)

ALA-HIS-ALA.1: 11 residues within 4Å: Chain A: K.42, S.43, T.44, D.121, N.122 Chain B: S.95, K.96, T.97, P.98, R.100, T.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.44, A:T.44 Water bridges: A:T.44

3 x DU2: 2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine(Non-covalent)

DU2.2: 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.95 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.117, A:A.119 Hydrogen bonds: A:N.103, A:I.117, A:I.117 Water bridges: A:L.107 pi-Stacking: A:F.46 DU2.4: 13 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.95 Ligands: SO4.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.46, B:Y.112, B:I.117, B:A.119 Hydrogen bonds: B:N.103, B:I.117, B:I.117 Water bridges: B:L.107 DU2.6: 14 residues within 4Å: Chain A: S.92, S.95 Chain C: F.46, L.88, N.103, G.106, L.107, I.108, Y.112, E.115, I.116, I.117, A.119 Ligands: SO4.3 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.46, C:Y.112, C:I.117, C:A.119 Hydrogen bonds: C:N.103, C:I.117, C:I.117 Water bridges: C:Y.112, C:Y.112

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

SO4.3: 4 residues within 4Å: Chain A: R.91, S.92, Q.138 Ligands: DU2.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:R.91, A:S.92, A:Q.138 Water bridges: C:L.107 SO4.5: 5 residues within 4Å: Chain A: L.107 Chain B: R.91, S.92, Q.138 Ligands: DU2.2 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.92, B:Q.138, A:L.107 Water bridges: B:R.91, B:S.92, A:L.107 Salt bridges: B:R.91 SO4.7: 4 residues within 4Å: Chain C: R.91, S.92, Q.138 Ligands: DU2.4 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:R.91, C:S.92, C:S.92, C:Q.138, C:Q.138 Water bridges: C:S.93, C:S.93 SO4.8: 4 residues within 4Å: Chain C: K.52, G.114, E.115, R.160 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.115 Salt bridges: C:K.52, C:R.160 SO4.9: 4 residues within 4Å: Chain C: G.111, Y.112, R.113, R.160 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.111, C:R.113 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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