SMTL ID : 5h4j.1

Crystal structure of Human dUTPase in complex with N-[(1R)-1-[3-(Cyclopentyloxy)-phenyl]-ethyl]-3-[(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)methoxy]-1-propanesulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-trimer

Ligands

3 x FKM: N-[(1R)-1-[3-(Cyclopentyloxy)-phenyl]-ethyl]-3-[(3,4-dihydro-2,4-dioxo-1(2H)-pyrimidinyl)methoxy]-1-propanesulfonamide(Non-covalent)

FKM.1: 14 residues within 4Å: Chain A: V.65, K.67, 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 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:V.65, A:K.67, A:N.108, A:V.112, C:A.90 Hydrogen bonds: A:G.99, A:G.110, A:G.110 Water bridges: C:S.86, C:S.86 FKM.5: 14 residues within 4Å: Chain A: S.86, G.87, A.90 Chain B: V.65, K.67, A.98, G.99, V.100, I.101, Y.105, N.108, V.109, G.110, V.112 10 PLIP interactions: 3 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.90, B:V.65, B:K.67, B:N.108, B:V.112 Water bridges: A:S.86, A:S.86 Hydrogen bonds: B:G.99, B:G.110, B:G.110 FKM.9: 14 residues within 4Å: Chain B: S.86, G.87, A.90 Chain C: V.65, K.67, A.98, G.99, V.100, I.101, 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:K.67, C:N.108, C:V.112, B:A.90 Hydrogen bonds: C:G.99, C:G.110, C:G.110 Water bridges: B:S.86, B:S.86

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: H.34 Ligands: IMD.3 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.34 ZN.6: 2 residues within 4Å: Chain B: H.34 Ligands: IMD.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:H.34 ZN.10: 2 residues within 4Å: Chain C: H.34 Ligands: IMD.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:H.34

3 x IMD: IMIDAZOLE(Non-covalent)

IMD.3: 4 residues within 4Å: Chain A: S.32, H.34, Y.54 Ligands: ZN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.54 IMD.7: 4 residues within 4Å: Chain B: S.32, H.34, Y.54 Ligands: ZN.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.54 IMD.11: 4 residues within 4Å: Chain C: S.32, H.34, Y.54 Ligands: ZN.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.54

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.4: 1 residues within 4Å: Chain A: H.92 No protein-ligand interaction detected (PLIP) DMS.8: 1 residues within 4Å: Chain B: H.92 No protein-ligand interaction detected (PLIP) DMS.12: 1 residues within 4Å: Chain C: H.92 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yano, W. et al., TAS-114, a First-in-Class Dual dUTPase/DPD Inhibitor, Demonstrates Potential to Improve Therapeutic Efficacy of Fluoropyrimidine-Based Chemotherapy. Mol. Cancer Ther. (2018)

Release Date

2017-11-01

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial

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