SMTL ID : 3ara.1

Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x MKH: 1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidine-2,4(1H,3H)-dione(Non-covalent)

MKH.1: 15 residues within 4Å: Chain A: V.65, K.67, V.82, A.98, G.99, V.100, I.101, Y.105, N.108, V.109, G.110, V.112 Chain C: S.86, A.90, K.91 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:V.65, A:V.65, A:Y.105, A:V.112, C:A.90, C:K.91 Hydrogen bonds: A:G.99, A:Y.105, A:G.110, A:G.110 Water bridges: A:K.67 MKH.3: 14 residues within 4Å: Chain A: S.86, A.90, K.91 Chain B: V.65, K.67, A.98, G.99, V.100, I.101, Y.105, N.108, V.109, G.110, V.112 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.65, B:V.65, B:Y.105, B:V.112, A:A.90, A:A.90, A:K.91 Hydrogen bonds: B:K.67, B:K.67, B:G.99, B:G.110, B:G.110 MKH.5: 13 residues within 4Å: Chain B: S.86, A.90, K.91 Chain C: V.65, V.82, A.98, G.99, V.100, Y.105, N.108, V.109, G.110, V.112 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.65, C:V.65, C:Y.105, C:V.112, B:A.90, B:A.90, B:K.91 Hydrogen bonds: C:G.99, C:G.110, C:G.110

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: Y.79, E.135 Chain B: Y.79, E.135 Chain C: Y.79, E.135 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.135, A:E.135, B:E.135, H2O.6 MG.4: 1 residues within 4Å: Chain B: H.34 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyakoshi, H. et al., Synthesis and discovery of N-carbonylpyrrolidine- or N-sulfonylpyrrolidine-containing uracil derivatives as potent human deoxyuridine triphosphatase inhibitors. J.Med.Chem. (2012)

Release Date

2010-12-08

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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