Zinc in PDB 5m0e: 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: 5m0e 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)	61.15 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.618, 61.729, 63.696, 103.43, 98.18, 93.50
R / Rfree (%)	18.1 / 22.3

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

Iodine	(I)	14 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 5m0e). 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: 5m0e:
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:Zn904 b:62.0 occ:1.00 OG1 A:THR209 2.0 22.4 1.0 OD1 A:ASP171 2.1 31.4 1.0 NE2 A:HIS359 2.2 17.9 1.0 OD2 A:ASP358 2.3 24.8 1.0 CG A:ASP171 2.8 30.9 1.0 OD2 A:ASP171 2.9 34.5 1.0 CB A:THR209 3.0 20.0 1.0 CG A:ASP358 3.0 21.8 1.0 CD2 A:HIS359 3.0 17.9 1.0 CE1 A:HIS359 3.1 18.0 1.0 OD1 A:ASP358 3.3 21.9 1.0 CG2 A:THR209 3.3 20.6 1.0 CA A:THR209 3.4 18.5 1.0 N A:THR209 3.8 17.7 1.0 CB A:ASP171 4.1 27.8 1.0 ND1 A:HIS359 4.1 17.7 1.0 CG A:HIS359 4.1 17.5 1.0 N A:GLY172 4.1 22.9 1.0 OD1 A:ASP311 4.1 26.1 1.0 O A:HOH1008 4.2 27.2 1.0 CB A:ASP358 4.2 20.9 1.0 CA A:ASP171 4.3 25.8 1.0 C17 A:7CR922 4.3 58.0 1.0 CE1 A:HIS474 4.4 18.4 1.0 CG A:ASP311 4.5 24.9 1.0 C A:ASP171 4.6 24.3 1.0 ZN A:ZN905 4.6 26.0 1.0 NE2 A:HIS474 4.6 18.7 1.0 N2 A:7CR922 4.7 55.9 1.0 C18 A:7CR922 4.7 59.9 1.0 C A:LYS208 4.7 17.3 1.0 C A:THR209 4.7 17.7 1.0 OD2 A:ASP311 4.8 24.4 1.0 CA A:GLY172 4.9 23.3 1.0 CB A:ASP311 5.0 25.0 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:Zn905 b:26.0 occ:1.00 NE2 A:HIS474 2.0 18.7 1.0 NE2 A:HIS315 2.1 27.4 1.0 N2 A:7CR922 2.3 55.9 1.0 OD1 A:ASP311 2.4 26.1 1.0 OD2 A:ASP311 2.4 24.4 1.0 CG A:ASP311 2.7 24.9 1.0 CE1 A:HIS474 3.0 18.4 1.0 CD2 A:HIS474 3.0 19.0 1.0 O3 A:7CR922 3.0 55.2 1.0 C19 A:7CR922 3.0 55.9 1.0 CD2 A:HIS315 3.0 27.6 1.0 CE1 A:HIS315 3.1 27.4 1.0 C18 A:7CR922 3.4 59.9 1.0 ND1 A:HIS474 4.1 18.6 1.0 C17 A:7CR922 4.1 58.0 1.0 CG A:HIS474 4.1 18.6 1.0 O A:HOH1008 4.2 27.2 1.0 CG A:HIS315 4.2 28.5 1.0 CB A:ASP311 4.2 25.0 1.0 ND1 A:HIS315 4.2 27.8 1.0 CE1 A:HIS359 4.2 18.0 1.0 O A:HOH1020 4.3 34.5 1.0 O4 A:7CR922 4.3 59.1 1.0 CE A:MET361 4.4 26.2 1.0 NE2 A:HIS359 4.4 17.9 1.0 OG1 A:THR209 4.4 22.4 1.0 OD1 A:ASP171 4.5 31.4 1.0 C20 A:7CR922 4.5 61.2 1.0 ZN A:ZN904 4.6 62.0 1.0 O A:ASP311 4.9 25.3 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