SMTL ID : 2y8c.1

Plasmodium falciparum dUTPase in complex with a trityl ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x DUQ: (2S)-2-[(2,4-dioxopyrimidin-1-yl)methyl]-N-(2-hydroxyethyl)-4-trityloxy-butanamide(Non-covalent)

DUQ.1: 14 residues within 4Å: Chain A: F.46, L.88, N.103, G.106, L.107, Y.112, E.115, I.116, I.117, A.119, R.160 Chain B: S.92, S.93, S.95 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:I.117, A:I.117, A:A.119 Hydrogen bonds: A:N.103, A:Y.112, A:I.117, A:I.117 DUQ.3: 15 residues within 4Å: Chain B: F.46, K.48, L.88, N.103, G.106, L.107, I.108, Y.112, E.115, I.117, A.119 Chain C: S.92, S.93, S.95, K.96 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.46, B:F.46, B:F.46, B:I.117, B:A.119, C:K.96 Hydrogen bonds: B:N.103, B:Y.112, B:I.117, B:I.117 Water bridges: B:A.119 pi-Stacking: B:F.46 DUQ.4: 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 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:F.46, C:F.46, C:F.46, C:I.117, C:I.117, C:A.119 Hydrogen bonds: C:N.103, C:Y.112, C:I.117, C:I.117 pi-Stacking: C:F.46

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

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baragana, B. et al., Beta-Branched Acyclic Nucleoside Analogues as Inhibitors of Plasmodium Falciparum Dutpase. Bioorg.Med.Chem. (2011)

Release Date

2012-03-07

Peptides

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE

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