Zinc in PDB 5m0m: 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: 5m0m 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)	75.27 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.995, 89.173, 77.289, 90.00, 103.12, 90.00
R / Rfree (%)	20.1 / 24.9

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

Iodine	(I)	12 atoms
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Structure-Based Evolution of A Hybrid Steroid Series of Autotaxin Inhibitors (pdb code 5m0m). 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: 5m0m:
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:Zn922 b:30.9 occ:1.00 O A:HOH1079 2.0 27.2 1.0 NE2 A:HIS315 2.1 31.3 1.0 NE2 A:HIS474 2.2 24.0 1.0 OD1 A:ASP311 2.3 31.4 1.0 OD2 A:ASP311 2.5 31.7 1.0 CG A:ASP311 2.7 31.6 1.0 CE1 A:HIS315 3.1 31.5 1.0 CE1 A:HIS474 3.1 23.5 1.0 CD2 A:HIS315 3.1 31.8 1.0 CD2 A:HIS474 3.2 24.4 1.0 CB A:ASP311 4.1 31.4 1.0 ND1 A:HIS315 4.2 32.2 1.0 CE1 A:HIS359 4.2 24.8 1.0 CG A:HIS315 4.2 32.2 1.0 ND1 A:HIS474 4.3 23.9 1.0 CG A:HIS474 4.3 24.4 1.0 OD1 A:ASP171 4.4 35.9 1.0 NE2 A:HIS359 4.5 24.4 1.0 CE A:MET361 4.6 29.3 1.0 O A:HOH1017 4.6 36.5 1.0 ZN A:ZN923 4.6 55.0 1.0 OG1 A:THR209 4.7 23.1 1.0 O A:ASP311 5.0 32.7 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:Zn923 b:55.0 occ:1.00 OG1 A:THR209 2.0 23.1 1.0 OD1 A:ASP171 2.1 35.9 1.0 NE2 A:HIS359 2.3 24.4 1.0 OD2 A:ASP358 2.5 25.1 1.0 CG A:ASP171 2.6 33.9 1.0 OD2 A:ASP171 2.7 35.3 1.0 CE1 A:HIS359 3.0 24.8 1.0 CB A:THR209 3.0 22.7 1.0 CG A:ASP358 3.2 24.2 1.0 CD2 A:HIS359 3.2 24.2 1.0 OD1 A:ASP358 3.3 23.9 1.0 CA A:THR209 3.4 22.4 1.0 CG2 A:THR209 3.5 22.7 1.0 N A:THR209 3.8 22.3 1.0 CB A:ASP171 3.9 33.0 1.0 N A:GLY172 4.0 29.6 1.0 ND1 A:HIS359 4.0 24.6 1.0 CG A:HIS359 4.2 24.1 1.0 CA A:ASP171 4.2 31.2 1.0 OD1 A:ASP311 4.4 31.4 1.0 C A:ASP171 4.5 30.5 1.0 CB A:ASP358 4.5 23.7 1.0 CE1 A:HIS474 4.5 23.5 1.0 CG A:ASP311 4.5 31.6 1.0 ZN A:ZN922 4.6 30.9 1.0 C A:LYS208 4.7 22.7 1.0 NE2 A:HIS474 4.7 24.0 1.0 C A:THR209 4.8 22.2 1.0 CA A:GLY172 4.8 29.2 1.0 OH A:TYR306 4.8 29.1 1.0 OD2 A:ASP311 4.9 31.7 1.0 CB A:ASP311 4.9 31.4 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