Zinc in PDB 8c4w: Crystal Structure of Rat Autotaxin and Compound Mey-002

All present enzymatic activity of Crystal Structure of Rat Autotaxin and Compound Mey-002:
3.1.4.39;

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-002, PDB code: 8c4w 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)	47.65 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.228, 62.863, 70.151, 98.99, 106.57, 99.51
R / Rfree (%)	19.6 / 23.6

The structure of Crystal Structure of Rat Autotaxin and Compound Mey-002 also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Iodine	(I)	9 atoms

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin and Compound Mey-002 (pdb code 8c4w). 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-002, PDB code: 8c4w:
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-002


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-002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:25.6 occ:1.00 O A:HOH1224 2.0 33.5 1.0 NE2 A:HIS315 2.2 27.1 1.0 NE2 A:HIS474 2.2 23.1 1.0 OD1 A:ASP311 2.2 25.1 1.0 OD2 A:ASP311 2.3 25.3 1.0 CG A:ASP311 2.6 24.8 1.0 CD2 A:HIS474 3.0 25.0 1.0 CD2 A:HIS315 3.1 26.0 1.0 CE1 A:HIS315 3.2 25.4 1.0 CE1 A:HIS474 3.3 25.0 1.0 O A:HOH1015 3.9 25.4 1.0 CB A:ASP311 4.1 28.8 1.0 CE1 A:HIS359 4.1 23.2 1.0 NE2 A:HIS359 4.2 21.8 1.0 CG A:HIS315 4.2 27.4 1.0 CG A:HIS474 4.2 21.8 1.0 ND1 A:HIS315 4.3 27.0 1.0 O A:HOH1023 4.3 27.6 1.0 ND1 A:HIS474 4.3 22.8 1.0 OD1 A:ASP171 4.4 22.5 1.0 O A:HOH1302 4.5 33.6 1.0 ZN A:ZN902 4.5 28.1 1.0 OG1 A:THR209 4.6 21.5 1.0 CE A:MET361 4.6 24.9 1.0 O A:HOH1016 4.7 35.3 1.0 O A:ASP311 4.9 25.7 1.0 CA A:ASP311 5.0 27.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin and Compound Mey-002


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-002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn902 b:28.1 occ:1.00 OD1 A:ASP171 1.9 22.5 1.0 OG1 A:THR209 2.0 21.5 1.0 OD2 A:ASP358 2.0 24.2 1.0 NE2 A:HIS359 2.2 21.8 1.0 CG A:ASP171 2.6 27.5 1.0 OD2 A:ASP171 2.8 25.6 1.0 CG A:ASP358 2.9 22.4 1.0 CD2 A:HIS359 2.9 23.9 1.0 CB A:THR209 3.0 20.3 1.0 OD1 A:ASP358 3.1 22.8 1.0 CE1 A:HIS359 3.2 23.2 1.0 CA A:THR209 3.4 21.5 1.0 CG2 A:THR209 3.5 23.7 1.0 N A:THR209 3.8 21.5 1.0 O A:HOH1015 3.9 25.4 1.0 CB A:ASP171 3.9 24.6 1.0 CG A:HIS359 4.0 25.0 1.0 O A:HOH1023 4.1 27.6 1.0 ND1 A:HIS359 4.1 22.2 1.0 N A:GLY172 4.1 22.4 1.0 OD1 A:ASP311 4.2 25.1 1.0 CB A:ASP358 4.2 21.4 1.0 CE1 A:HIS474 4.3 25.0 1.0 CA A:ASP171 4.3 23.4 1.0 CG A:ASP311 4.4 24.8 1.0 NE2 A:HIS474 4.5 23.1 1.0 ZN A:ZN901 4.5 25.6 1.0 C A:ASP171 4.6 25.8 1.0 OD2 A:ASP311 4.6 25.3 1.0 C A:LYS208 4.7 22.2 1.0 C A:THR209 4.8 21.6 1.0 CB A:ASP311 4.8 28.8 1.0 CA A:GLY172 4.9 25.5 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