Zinc in PDB 5ebt: Tankyrase 1 with Phthalazinone 2

All present enzymatic activity of Tankyrase 1 with Phthalazinone 2:
2.4.2.30;

The structure of Tankyrase 1 with Phthalazinone 2, PDB code: 5ebt was solved by S.L.Kazmirski, J.Johannes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.35 / 2.24
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.733, 151.189, 57.224, 90.00, 96.28, 90.00
R / Rfree (%)	17.1 / 20.8

The structure of Tankyrase 1 with Phthalazinone 2 also contains other interesting chemical elements:

Fluorine

(F)

20 atoms

The binding sites of Zinc atom in the Tankyrase 1 with Phthalazinone 2 (pdb code 5ebt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Tankyrase 1 with Phthalazinone 2, PDB code: 5ebt:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1403 b:31.9 occ:1.00 ND1 A:HIS1237 2.2 33.5 1.0 SG A:CYS1245 2.2 28.4 1.0 SG A:CYS1234 2.3 29.8 1.0 SG A:CYS1242 2.3 32.2 1.0 CE1 A:HIS1237 3.1 33.7 1.0 CG A:HIS1237 3.2 32.2 1.0 CB A:CYS1234 3.3 24.8 1.0 CB A:CYS1245 3.3 23.9 1.0 CB A:CYS1242 3.3 26.8 1.0 CB A:HIS1237 3.6 29.0 1.0 N A:HIS1237 3.8 29.4 1.0 N A:CYS1245 4.1 23.7 1.0 CA A:HIS1237 4.3 29.2 1.0 NE2 A:HIS1237 4.3 35.3 1.0 CA A:CYS1245 4.3 24.1 1.0 CB A:THR1236 4.3 37.0 1.0 CD2 A:HIS1237 4.4 35.5 1.0 CA A:CYS1234 4.7 25.5 1.0 C A:THR1236 4.7 35.4 1.0 CA A:CYS1242 4.7 25.7 1.0 CA A:THR1236 4.9 32.4 1.0

Zinc binding site 2 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1402 b:25.4 occ:1.00 ND1 B:HIS1237 2.1 28.4 1.0 SG B:CYS1245 2.2 27.0 1.0 SG B:CYS1234 2.2 29.8 1.0 SG B:CYS1242 2.3 24.5 1.0 CE1 B:HIS1237 3.1 27.1 1.0 CG B:HIS1237 3.2 28.1 1.0 CB B:CYS1234 3.3 24.4 1.0 CB B:CYS1242 3.3 19.6 1.0 CB B:CYS1245 3.4 22.2 1.0 CB B:HIS1237 3.5 26.1 1.0 N B:HIS1237 3.8 26.4 1.0 N B:CYS1245 4.0 21.4 1.0 NE2 B:HIS1237 4.3 28.7 1.0 CA B:HIS1237 4.3 27.0 1.0 CA B:CYS1245 4.3 21.2 1.0 CD2 B:HIS1237 4.3 29.5 1.0 CB B:THR1236 4.4 37.7 1.0 CA B:CYS1234 4.7 24.0 1.0 C B:THR1236 4.7 29.8 1.0 CA B:CYS1242 4.7 19.0 1.0 CA B:THR1236 4.9 27.0 1.0 CB B:ILE1244 5.0 24.0 1.0

Zinc binding site 3 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1403 b:22.6 occ:1.00 ND1 C:HIS1237 2.1 25.6 1.0 SG C:CYS1234 2.2 22.9 1.0 SG C:CYS1245 2.2 26.8 1.0 SG C:CYS1242 2.3 20.0 1.0 CE1 C:HIS1237 3.1 25.0 1.0 CG C:HIS1237 3.2 25.4 1.0 CB C:CYS1234 3.3 19.3 1.0 CB C:CYS1245 3.3 22.1 1.0 CB C:CYS1242 3.3 15.3 1.0 CB C:HIS1237 3.6 22.3 1.0 N C:HIS1237 3.8 24.8 1.0 N C:CYS1245 4.0 21.7 1.0 CA C:CYS1245 4.3 22.2 1.0 NE2 C:HIS1237 4.3 26.5 1.0 CA C:HIS1237 4.3 23.3 1.0 CD2 C:HIS1237 4.3 27.6 1.0 CB C:THR1236 4.4 30.4 1.0 O C:HOH1553 4.7 44.2 1.0 CA C:CYS1234 4.7 21.1 1.0 O C:HOH1529 4.7 16.3 1.0 CA C:CYS1242 4.7 16.4 1.0 C C:THR1236 4.8 29.8 1.0 CA C:THR1236 4.9 26.8 1.0 CB C:ILE1244 5.0 25.1 1.0

Zinc binding site 4 out of 4 in the Tankyrase 1 with Phthalazinone 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tankyrase 1 with Phthalazinone 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1401 b:35.0 occ:1.00 SG D:CYS1245 2.2 34.4 1.0 SG D:CYS1242 2.2 31.7 1.0 ND1 D:HIS1237 2.2 38.7 1.0 SG D:CYS1234 2.3 33.7 1.0 CE1 D:HIS1237 3.1 38.9 1.0 CB D:CYS1245 3.2 29.2 1.0 CB D:CYS1234 3.3 29.2 1.0 CB D:CYS1242 3.3 26.6 1.0 CG D:HIS1237 3.3 38.0 1.0 CB D:HIS1237 3.7 34.4 1.0 N D:CYS1245 3.9 30.1 1.0 O D:HOH1557 3.9 27.2 1.0 N D:HIS1237 4.0 35.1 1.0 CA D:CYS1245 4.1 29.9 1.0 NE2 D:HIS1237 4.3 40.8 1.0 CB D:THR1236 4.4 47.1 1.0 CD2 D:HIS1237 4.4 41.1 1.0 CA D:HIS1237 4.4 34.7 1.0 O D:HOH1510 4.5 37.3 1.0 CA D:CYS1234 4.7 30.4 1.0 CA D:CYS1242 4.7 26.8 1.0 CB D:ILE1244 4.8 33.6 1.0 C D:THR1236 4.9 40.7 1.0

J.W.Johannes, L.Almeida, K.Daly, A.D.Ferguson, S.E.Grosskurth, H.Guan, T.Howard, S.Ioannidis, S.Kazmirski, M.L.Lamb, N.A.Larsen, P.D.Lyne, K.Mikule, C.Ogoe, B.Peng, P.Petteruti, J.A.Read, N.Su, M.Sylvester, S.Throner, W.Wang, X.Wang, J.Wu, Q.Ye, Y.Yu, X.Zheng, D.A.Scott. Discovery of AZ0108, An Orally Bioavailable Phthalazinone Parp Inhibitor That Blocks Centrosome Clustering. Bioorg.Med.Chem.Lett. V. 25 5743 2015.
ISSN: ESSN 1464-3405
PubMed: 26546219
DOI: 10.1016/J.BMCL.2015.10.079