SMTL ID : 3t70.1

5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

1 x GLY- HIS- GLY: PEPTIDE GLY-HIS-GLY(Non-covalent)

GLY-HIS-GLY.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 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.44, A:T.44, A:T.44, B:R.100 Water bridges: A:T.44, B:T.123

3 x DU4: 2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine(Non-covalent)

DU4.2: 14 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 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: 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 Water bridges: A:L.107, A:D.109, A:Y.112, A:A.119, B:S.92, B:S.92 pi-Stacking: A:F.46, A:F.46 DU4.4: 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: SO4.9 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.46, B:F.46, B:F.46, B:I.108, 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, B:D.109, C:S.92 DU4.8: 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 16 PLIP interactions: 16 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 Water bridges: C:L.107, C:D.109, C:Y.112, C:Y.112, C:Y.112, C:Y.112 pi-Stacking: C:F.46

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

SO4.3: 5 residues within 4Å: Chain A: R.91, S.92, Q.138 Chain C: L.107 Ligands: DU4.8 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 SO4.5: 3 residues within 4Å: Chain B: R.91, S.92, Q.138 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.92, B:Q.138 Water bridges: B:D.30, B:R.91, B:S.92, B:S.92, B:S.93, B:S.93, A:L.107 Salt bridges: B:R.91 SO4.6: 2 residues within 4Å: Chain B: Q.126, E.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.127 SO4.7: 2 residues within 4Å: Chain B: K.132, N.133 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.133 Salt bridges: B:K.132 SO4.9: 5 residues within 4Å: Chain B: D.109 Chain C: R.91, S.92, Q.138 Ligands: DU4.4 7 PLIP interactions: 7 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 Salt bridges: C:R.91 SO4.10: 5 residues within 4Å: Chain C: G.111, Y.112, R.113, G.114, 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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