SMTL ID : 3arn.1

Human dUTPase in complex with novel uracil derivative

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x MSJ: N-{5-[(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)methoxy]-2-methylpentan-2-yl}benzenesulfonamide(Non-covalent)

MSJ.1: 14 residues within 4Å: Chain A: V.65, A.98, G.99, V.100, I.101, Y.105, N.108, V.109, G.110, V.112 Chain C: S.86, G.87, A.90, K.91 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.65, A:V.112, C:A.90 Hydrogen bonds: A:G.99, A:G.110, A:G.110, C:K.91 Water bridges: C:S.86 MSJ.5: 14 residues within 4Å: Chain A: S.86, G.87, A.90, K.91 Chain B: V.65, A.98, G.99, V.100, I.101, Y.105, N.108, V.109, G.110, V.112 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:A.90, B:V.65, B:V.112 Hydrogen bonds: A:K.91, B:G.99, B:G.110, B:G.110 Water bridges: A:S.86 MSJ.8: 14 residues within 4Å: Chain B: S.86, G.87, A.90, K.91 Chain C: V.65, A.98, G.99, V.100, I.101, Y.105, N.108, V.109, G.110, V.112 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:V.65, C:V.112, B:A.90 Hydrogen bonds: C:G.99, C:G.110, C:G.110 Water bridges: B:S.86

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.95 Chain B: D.95 Chain C: D.95 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.4, H2O.4, H2O.9, H2O.9, H2O.15 MG.3: 1 residues within 4Å: Chain A: H.92 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.92 MG.4: 3 residues within 4Å: Chain A: E.135 Chain B: E.135 Chain C: E.135 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:E.135, C:E.135, B:E.135, H2O.11 MG.6: 1 residues within 4Å: Chain B: H.34 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.34 MG.7: 1 residues within 4Å: Chain B: H.92 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.92 MG.9: 1 residues within 4Å: Chain C: H.92 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.92

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyahara, S. et al., Discovery of a novel class of potent human deoxyuridine triphosphatase inhibitors remarkably enhancing the antitumor activity of thymidylate synthase inhibitors. J.Med.Chem. (2012)

Release Date

2010-12-15

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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