Zinc in PDB 5olb: Crystal Structure of Autotaxin in Complex with Pf-8380

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with Pf-8380:
3.1.4.39;

The structure of Crystal Structure of Autotaxin in Complex with Pf-8380, PDB code: 5olb was solved by S.Hoerer, A.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.65 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	124.734, 100.045, 78.778, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 19.1

The structure of Crystal Structure of Autotaxin in Complex with Pf-8380 also contains other interesting chemical elements:

Potassium	(K)	1 atom
Calcium	(Ca)	2 atoms
Chlorine	(Cl)	3 atoms
Sodium	(Na)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of Autotaxin in Complex with Pf-8380 (pdb code 5olb). 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 Autotaxin in Complex with Pf-8380, PDB code: 5olb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with Pf-8380


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 Autotaxin in Complex with Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn915 b:19.0 occ:1.00 N31 A:6ZO925 1.9 42.7 1.0 NE2 A:HIS315 2.0 19.5 1.0 NE2 A:HIS474 2.0 16.4 1.0 OD1 A:ASP311 2.3 19.1 1.0 OD2 A:ASP311 2.5 22.5 1.0 CG A:ASP311 2.7 20.8 1.0 C30 A:6ZO925 2.8 43.8 1.0 CD2 A:HIS315 3.0 20.1 1.0 CE1 A:HIS315 3.0 19.8 1.0 CD2 A:HIS474 3.0 16.6 1.0 CE1 A:HIS474 3.1 15.9 1.0 C28 A:6ZO925 3.1 42.8 1.0 O32 A:6ZO925 3.2 44.2 1.0 C27 A:6ZO925 3.7 40.9 1.0 O A:HOH1006 3.8 22.7 1.0 O29 A:6ZO925 4.1 44.0 1.0 CG A:HIS315 4.1 19.4 1.0 ND1 A:HIS315 4.1 21.0 1.0 CG A:HIS474 4.2 15.5 1.0 C26 A:6ZO925 4.2 43.3 1.0 ND1 A:HIS474 4.2 16.4 1.0 CB A:ASP311 4.2 15.4 1.0 CE1 A:HIS359 4.2 15.3 1.0 O A:HOH1335 4.4 42.8 1.0 CE A:MET361 4.4 17.2 1.0 O A:HOH1162 4.5 47.9 1.0 NE2 A:HIS359 4.5 15.4 1.0 OD1 A:ASP171 4.5 14.5 1.0 OG1 A:THR209 4.6 21.1 1.0 ZN A:ZN916 4.6 19.4 1.0 O A:ASP311 4.8 16.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with Pf-8380


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 Autotaxin in Complex with Pf-8380 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn916 b:19.4 occ:1.00 OD1 A:ASP171 2.0 14.5 1.0 OG1 A:THR209 2.0 21.1 1.0 OD2 A:ASP358 2.0 15.7 1.0 NE2 A:HIS359 2.0 15.4 1.0 CG A:ASP171 2.6 17.2 1.0 OD2 A:ASP171 2.8 20.7 1.0 CG A:ASP358 2.9 15.9 1.0 CD2 A:HIS359 2.9 15.5 1.0 CE1 A:HIS359 3.0 15.3 1.0 CB A:THR209 3.0 19.4 1.0 OD1 A:ASP358 3.1 15.1 1.0 CA A:THR209 3.4 13.9 1.0 CG2 A:THR209 3.5 16.0 1.0 N A:THR209 3.7 14.3 1.0 CB A:ASP171 4.0 15.7 1.0 C27 A:6ZO925 4.0 40.9 1.0 CG A:HIS359 4.0 14.7 1.0 ND1 A:HIS359 4.1 15.7 1.0 O A:HOH1006 4.1 22.7 1.0 OD1 A:ASP311 4.1 19.1 1.0 N A:GLY172 4.1 15.2 1.0 CB A:ASP358 4.3 14.6 1.0 CG A:ASP311 4.4 20.8 1.0 CA A:ASP171 4.4 14.6 1.0 CE1 A:HIS474 4.4 15.9 1.0 C A:LYS208 4.6 16.8 0.6 C A:LYS208 4.6 16.8 0.4 ZN A:ZN915 4.6 19.0 1.0 C A:ASP171 4.6 18.6 1.0 NE2 A:HIS474 4.7 16.4 1.0 C28 A:6ZO925 4.7 42.8 1.0 C25 A:6ZO925 4.7 41.0 1.0 C A:THR209 4.8 16.9 1.0 OD2 A:ASP311 4.8 22.5 1.0 CB A:ASP311 4.9 15.4 1.0 N31 A:6ZO925 4.9 42.7 1.0 CA A:GLY172 4.9 14.9 1.0

C.A.Kuttruff, M.Ferrara, T.Bretschneider, S.Hoerer, S.Handschuh, B.Nosse, H.Romig, P.Nicklin, G.J.Roth. Discovery of Bi-2545: A Novel Autotaxin Inhibitor That Significantly Reduces Lpa Levels in Vivo. Acs Med Chem Lett V. 8 1252 2017.
ISSN: ISSN 1948-5875
PubMed: 29259743
DOI: 10.1021/ACSMEDCHEMLETT.7B00312