Zinc in PDB 5m0d: 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: 5m0d 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)	75.34 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.927, 88.012, 77.356, 90.00, 103.10, 90.00
R / Rfree (%)	22.5 / 27

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

Iodine	(I)	9 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 5m0d). 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: 5m0d:
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:Zn918 b:75.5 occ:1.00 NE2 A:HIS474 2.3 48.6 1.0 OD2 A:ASP311 2.3 59.5 1.0 NE2 A:HIS315 2.4 63.1 1.0 OD1 A:ASP311 2.8 58.7 1.0 CG A:ASP311 2.9 58.9 1.0 CE1 A:HIS474 3.0 47.8 1.0 CE1 A:HIS315 3.2 63.3 1.0 CD2 A:HIS474 3.4 48.8 1.0 CD2 A:HIS315 3.6 64.0 1.0 ND1 A:HIS474 4.2 47.5 1.0 CB A:ASP311 4.4 58.7 1.0 ND1 A:HIS315 4.4 64.4 1.0 OG1 A:THR209 4.4 44.7 1.0 CG A:HIS474 4.4 48.1 1.0 CE1 A:HIS359 4.5 45.8 1.0 CG A:HIS315 4.6 64.8 1.0 ZN A:ZN919 4.7 0.3 1.0 NE2 A:HIS359 4.7 45.2 1.0 OD2 A:ASP171 4.9 52.1 1.0 OD1 A:ASP171 4.9 51.0 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:Zn919 b:0.3 occ:1.00 OG1 A:THR209 1.8 44.7 1.0 OD1 A:ASP171 1.9 51.0 1.0 NE2 A:HIS359 2.4 45.2 1.0 OD2 A:ASP358 2.4 44.3 1.0 CG A:ASP171 2.7 51.3 1.0 CB A:THR209 2.8 44.3 1.0 OD2 A:ASP171 3.0 52.1 1.0 CE1 A:HIS359 3.1 45.8 1.0 CG A:ASP358 3.1 43.9 1.0 CA A:THR209 3.1 43.5 1.0 CG2 A:THR209 3.2 44.3 1.0 OD1 A:ASP358 3.3 44.3 1.0 CD2 A:HIS359 3.4 44.5 1.0 N A:THR209 3.6 43.6 1.0 CB A:ASP171 4.0 51.1 1.0 ND1 A:HIS359 4.2 45.5 1.0 OD2 A:ASP311 4.2 59.5 1.0 N A:GLY172 4.3 50.4 1.0 CG A:HIS359 4.3 44.6 1.0 CA A:ASP171 4.4 50.4 1.0 CB A:ASP358 4.4 43.2 1.0 C A:LYS208 4.4 43.0 1.0 CE1 A:HIS474 4.5 47.8 1.0 C A:THR209 4.5 43.2 1.0 CG A:ASP311 4.6 58.9 1.0 OH A:TYR306 4.7 51.9 1.0 C A:ASP171 4.7 50.8 1.0 ZN A:ZN918 4.7 75.5 1.0 NE2 A:HIS474 4.8 48.6 1.0 O A:LYS208 4.9 42.5 1.0 O A:THR209 4.9 42.9 1.0 OD1 A:ASP311 5.0 58.7 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