Zinc in PDB 5m0s: Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors

All present enzymatic activity of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors:
3.1.4.39;

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0s was solved by W.-J.Keune, T.Heidebrecht, A.Perrakis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.29 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.826, 88.857, 77.293, 90.00, 103.08, 90.00
R / Rfree (%)	23.8 / 28.6

The structure of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors also contains other interesting chemical elements:

Iodine	(I)	13 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors (pdb code 5m0s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors, PDB code: 5m0s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn911 b:52.4 occ:1.00 O A:HOH1060 2.0 63.9 1.0 NE2 A:HIS315 2.1 48.2 1.0 NE2 A:HIS474 2.3 38.5 1.0 OD2 A:ASP311 2.4 44.2 1.0 OD1 A:ASP311 2.4 43.5 1.0 CG A:ASP311 2.7 43.8 1.0 CD2 A:HIS315 3.1 49.1 1.0 CE1 A:HIS315 3.1 48.5 1.0 CD2 A:HIS474 3.2 38.7 1.0 CE1 A:HIS474 3.4 37.8 1.0 O A:HOH1002 3.5 48.7 1.0 CB A:ASP311 4.2 43.7 1.0 ND1 A:HIS315 4.2 49.6 1.0 CG A:HIS315 4.2 50.0 1.0 CE1 A:HIS359 4.4 36.0 1.0 CG A:HIS474 4.4 38.1 1.0 OG1 A:THR209 4.4 33.5 1.0 ND1 A:HIS474 4.4 37.5 1.0 ZN A:ZN912 4.5 0.1 1.0 OD1 A:ASP171 4.6 39.7 1.0 CE A:MET361 4.6 40.4 1.0 NE2 A:HIS359 4.8 35.5 1.0

Zinc binding site 2 out of 2 in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn912 b:0.1 occ:1.00 OG1 A:THR209 1.9 33.5 1.0 OD1 A:ASP171 1.9 39.7 1.0 OD2 A:ASP358 2.5 34.3 1.0 NE2 A:HIS359 2.5 35.5 1.0 CG A:ASP171 2.7 39.7 1.0 CB A:THR209 2.8 32.9 1.0 OD2 A:ASP171 2.9 40.5 1.0 CE1 A:HIS359 3.0 36.0 1.0 CG2 A:THR209 3.1 32.9 1.0 CA A:THR209 3.2 32.2 1.0 CG A:ASP358 3.3 34.0 1.0 OD1 A:ASP358 3.5 34.5 1.0 CD2 A:HIS359 3.6 34.9 1.0 N A:THR209 3.6 32.3 1.0 O A:HOH1002 4.0 48.7 1.0 CB A:ASP171 4.0 39.5 1.0 ND1 A:HIS359 4.1 35.7 1.0 N A:GLY172 4.2 38.9 1.0 CA A:ASP171 4.4 38.8 1.0 CG A:HIS359 4.5 35.0 1.0 ZN A:ZN911 4.5 52.4 1.0 CE1 A:HIS474 4.5 37.8 1.0 OD1 A:ASP311 4.5 43.5 1.0 C A:THR209 4.5 31.9 1.0 C A:LYS208 4.5 32.0 1.0 NE2 A:HIS474 4.6 38.5 1.0 CG A:ASP311 4.6 43.8 1.0 C A:ASP171 4.6 39.2 1.0 OH A:TYR306 4.7 38.7 1.0 CB A:ASP358 4.7 33.4 1.0 OD2 A:ASP311 4.7 44.2 1.0

W.J.Keune, F.Potjewyd, T.Heidebrecht, F.Salgado-Polo, S.J.Macdonald, L.Chelvarajan, A.Abdel Latif, S.Soman, A.J.Morris, A.J.Watson, C.Jamieson, A.Perrakis. Rational Design of Autotaxin Inhibitors By Structural Evolution of Endogenous Modulators. J. Med. Chem. V. 60 2006 2017.
ISSN: ISSN 1520-4804
PubMed: 28165241
DOI: 10.1021/ACS.JMEDCHEM.6B01743