Zinc in PDB 8c7r: Crystal Structure of Rat Autotaxin and Compound Mey-003

All present enzymatic activity of Crystal Structure of Rat Autotaxin and Compound Mey-003:
3.1.4.39;

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-003, PDB code: 8c7r was solved by M.C.Eymery, A.A.Mccarthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.64 / 2.53
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.529, 61.843, 63.85, 104.01, 98.43, 93.27
R / Rfree (%)	20.5 / 25.4

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-003 also contains other interesting chemical elements:

Iodine	(I)	4 atoms
Calcium	(Ca)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin and Compound Mey-003 (pdb code 8c7r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Rat Autotaxin and Compound Mey-003, PDB code: 8c7r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin and Compound Mey-003


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Rat Autotaxin and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn903 b:46.2 occ:1.00 OD2 A:ASP311 1.6 49.6 1.0 NE2 A:HIS474 2.2 36.6 1.0 NE2 A:HIS315 2.3 38.9 1.0 CG A:ASP311 2.4 42.9 1.0 OD1 A:ASP311 2.6 46.4 1.0 CD2 A:HIS315 3.2 40.3 1.0 CE1 A:HIS474 3.2 31.8 1.0 CD2 A:HIS474 3.2 35.3 1.0 CE1 A:HIS315 3.3 34.3 1.0 CB A:ASP311 3.8 36.1 1.0 CE1 A:HIS359 4.0 47.7 1.0 NE2 A:HIS359 4.3 49.3 1.0 OG1 A:THR209 4.3 49.4 1.0 ND1 A:HIS474 4.3 39.2 1.0 CG A:HIS315 4.3 36.1 1.0 ND1 A:HIS315 4.4 39.5 1.0 CG A:HIS474 4.4 36.5 1.0 ZN A:ZN904 4.4 90.3 1.0 OD1 A:ASP171 4.4 58.5 1.0 CE A:MET361 4.5 35.2 1.0 CA A:ASP311 4.8 39.7 1.0 O A:ASP311 4.8 43.7 1.0 C A:ASP311 4.9 44.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin and Compound Mey-003


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Rat Autotaxin and Compound Mey-003 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn904 b:90.3 occ:1.00 OD1 A:ASP171 1.9 58.5 1.0 OG1 A:THR209 1.9 49.4 1.0 OD2 A:ASP358 2.2 46.7 1.0 NE2 A:HIS359 2.3 49.3 1.0 CG2 A:THR209 2.4 45.6 1.0 CB A:THR209 2.4 42.3 1.0 CG A:ASP171 2.8 44.4 1.0 CA A:THR209 3.0 36.5 1.0 OD2 A:ASP171 3.1 52.0 1.0 CD2 A:HIS359 3.2 49.5 1.0 CE1 A:HIS359 3.3 47.7 1.0 CG A:ASP358 3.3 35.0 1.0 N A:THR209 3.6 34.0 1.0 OD1 A:ASP358 3.8 39.4 1.0 OD2 A:ASP311 4.1 49.6 1.0 CB A:ASP171 4.2 40.6 1.0 ND1 A:HIS359 4.3 50.0 1.0 CG A:HIS359 4.3 41.0 1.0 CG A:ASP311 4.4 42.9 1.0 C A:THR209 4.4 31.6 1.0 ZN A:ZN903 4.4 46.2 1.0 CE1 A:HIS474 4.5 31.8 1.0 CB A:ASP358 4.5 33.4 1.0 C A:LYS208 4.5 31.5 1.0 CA A:ASP171 4.6 40.0 1.0 NE2 A:HIS474 4.7 36.6 1.0 N A:GLY172 4.7 38.1 1.0 OD1 A:ASP311 4.8 46.4 1.0 O A:THR209 4.9 32.8 1.0 CB A:ASP311 4.9 36.1 1.0 C A:ASP171 5.0 37.8 1.0

M.C.Eymery, K.A.Nguyen, S.Basu, J.Hausmann, V.K.T.Nguyen, H.P.Seidel, L.Gutierrez, A.Boumendjel, A.A.Mccarthy. Discovery of Potent Chromone-Based Autotaxin Inhibitors Inspired By Cannabinoids Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115944