SMTL ID : 4hhy.3 (3 other biounits)

Crystal structure of PARP catalytic domain in complex with novel inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

1 x 15R: (9aR)-1-[(1-{2-fluoro-5-[(4-oxo-3,4-dihydrophthalazin-1-yl)methyl]benzoyl}piperidin-4-yl)carbonyl]-1,2,3,8,9,9a-hexahydro-7H-benzo[de][1,7]naphthyridin-7-one(Non-covalent)

15R.1: 19 residues within 4Å: Chain A: L.113, D.114, H.206, G.207, R.222, I.223, A.224, G.232, Y.233, G.238, I.239, Y.240, F.241, A.242, K.247, S.248, Y.251, E.332 Ligands: PEG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.113, A:A.224, A:Y.240, A:Y.240, A:Y.251, A:Y.251, A:E.332 Hydrogen bonds: A:G.207, A:G.207, A:I.223 pi-Cation interactions: A:R.222

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

SO4.2: 4 residues within 4Å: Chain A: K.247, L.328, L.329, Y.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.329, A:Y.330, A:E.332 Salt bridges: A:K.247

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 9 residues within 4Å: Chain A: D.114, S.208, G.215, I.216, Q.219, G.220, L.221, R.222 Ligands: 15R.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.114, A:S.208, A:S.208, A:R.222, A:R.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, N. et al., Design, Synthesis, and Biological Evaluation of a Series of Benzo[de][1,7]naphthyridin-7(8H)-ones Bearing a Functionalized Longer Chain Appendage as Novel PARP1 Inhibitors. J.Med.Chem. (2013)

Release Date

2013-03-27

Peptides

Poly [ADP-ribose] polymerase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly [ADP-ribose] polymerase 1

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