SMTL ID : 6hml.1

POLYADPRIBOSYL GLYCOSIDASE IN COMPLEX WITH PDD00017299

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x 73L: 1-[(2,4-dimethyl-1,3-thiazol-5-yl)methyl]-6-[[(1-methylcyclopropyl)amino]-bis(oxidanyl)-$l^{4}-sulfanyl]-3-[(1-methylpyrazol-4-yl)methyl]quinazoline-2,4-dione(Non-covalent)

73L.1: 18 residues within 4Å: Chain A: Y.277, E.278, G.279, T.280, I.281, E.282, Q.309, I.312, R.313, I.316, Y.347, Y.350, N.424, T.456, F.457, G.458, D.459 Ligands: GOL.7 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.280, A:I.312, A:R.313 Hydrogen bonds: A:I.281, A:E.282, A:Q.309 pi-Stacking: A:Y.350, A:F.457, A:F.457, A:F.457

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

DMS.2: 6 residues within 4Å: Chain A: Y.76, L.93, K.114, Y.115, N.116, V.117 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.117 Water bridges: A:A.118 DMS.3: 6 residues within 4Å: Chain A: P.31, V.37, I.39, R.40, V.41, F.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.41, A:D.42 pi-Cation interactions: A:F.53 DMS.4: 5 residues within 4Å: Chain A: L.28, L.29, V.41, L.44, D.368 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.29

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: E.264, R.265, C.266, E.267, T.479, G.481, D.482, K.485 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.266, A:T.479 Water bridges: A:D.482 GOL.6: 8 residues within 4Å: Chain A: E.282, Q.286, Q.343, H.360, E.361, D.362, G.363, S.364 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.361, A:D.362, A:G.363 Water bridges: A:Q.343, A:T.374 GOL.7: 5 residues within 4Å: Chain A: T.280, E.283, Y.347, T.348 Ligands: 73L.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.347, A:Y.347 Water bridges: A:Y.347, A:G.349

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

SO4.8: 5 residues within 4Å: Chain A: R.90, Y.119, P.198, R.199, N.201 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.119, A:R.199, A:N.201, A:N.201 Water bridges: A:R.90, A:R.90, A:R.90, A:R.199 Salt bridges: A:R.90, A:R.199 SO4.9: 2 residues within 4Å: Chain A: P.393, R.397 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.394 Salt bridges: A:R.397

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Waszkowycz, B. et al., Cell-Active Small Molecule Inhibitors of the DNA-Damage Repair Enzyme Poly(ADP-ribose) Glycohydrolase (PARG): Discovery and Optimization of Orally Bioavailable Quinazolinedione Sulfonamides. J.Med.Chem. (2018)

Release Date

2018-11-14

Peptides

Poly(ADP-ribose) glycohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly(ADP-ribose) glycohydrolase

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