Zinc in PDB 6leh: Crystal Structure of Autotaxin in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of Autotaxin in Complex with An Inhibitor:
3.1.4.39;

The structure of Crystal Structure of Autotaxin in Complex with An Inhibitor, PDB code: 6leh was solved by H.Nishimasu, N.Osamu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.07 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.507, 94.145, 75.556, 90.00, 93.92, 90.00
R / Rfree (%)	18.9 / 23.7

The structure of Crystal Structure of Autotaxin in Complex with An Inhibitor also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Crystal Structure of Autotaxin in Complex with An Inhibitor (pdb code 6leh). 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 An Inhibitor, PDB code: 6leh:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Autotaxin in Complex with An Inhibitor


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn910 b:33.0 occ:1.00 OG1 A:THR209 1.8 33.5 1.0 OD1 A:ASP171 1.9 24.4 1.0 NE2 A:HIS359 2.2 23.8 1.0 OD2 A:ASP358 2.4 31.8 1.0 CG A:ASP171 2.6 27.1 1.0 OD2 A:ASP171 2.8 30.1 1.0 CD2 A:HIS359 2.9 22.6 1.0 CB A:THR209 2.9 26.9 1.0 CE1 A:HIS359 3.2 25.5 1.0 CG A:ASP358 3.3 27.2 1.0 OD1 A:ASP358 3.4 27.8 1.0 CG2 A:THR209 3.4 26.5 1.0 CA A:THR209 3.4 22.0 1.0 O1 A:SO4915 3.7 29.8 1.0 N A:THR209 3.9 24.5 1.0 O3 A:SO4915 3.9 33.3 1.0 OD1 A:ASP311 4.0 28.3 1.0 CB A:ASP171 4.0 25.7 1.0 CG A:HIS359 4.1 22.9 1.0 N A:GLY172 4.2 24.0 1.0 O A:HOH1174 4.2 36.8 1.0 ND1 A:HIS359 4.2 24.9 1.0 CG A:ASP311 4.3 28.8 1.0 CA A:ASP171 4.4 26.3 1.0 CE1 A:HIS474 4.4 25.8 1.0 S A:SO4915 4.4 39.0 1.0 ZN A:ZN911 4.5 24.2 1.0 C A:ASP171 4.6 27.3 1.0 NE2 A:HIS474 4.6 27.7 1.0 CB A:ASP358 4.6 26.6 1.0 CB A:ASP311 4.7 29.0 1.0 C A:LYS208 4.7 23.3 1.0 OD2 A:ASP311 4.7 32.0 1.0 C A:THR209 4.8 23.4 1.0 CA A:GLY172 4.9 26.5 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Autotaxin in Complex with An Inhibitor


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 An Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn911 b:24.2 occ:1.00 O3 A:SO4915 1.9 33.3 1.0 NE2 A:HIS315 1.9 27.2 1.0 NE2 A:HIS474 1.9 27.7 1.0 OD1 A:ASP311 2.1 28.3 1.0 OD2 A:ASP311 2.6 32.0 1.0 CG A:ASP311 2.6 28.8 1.0 CE1 A:HIS315 2.9 27.1 1.0 CE1 A:HIS474 2.9 25.8 1.0 O2 A:SO4915 2.9 38.5 1.0 S A:SO4915 2.9 39.0 1.0 CD2 A:HIS315 2.9 27.3 1.0 CD2 A:HIS474 3.0 21.7 1.0 O1 A:SO4915 3.7 29.8 1.0 ND1 A:HIS315 4.0 25.4 1.0 ND1 A:HIS474 4.0 25.1 1.0 CG A:HIS315 4.0 29.6 1.0 CG A:HIS474 4.1 22.1 1.0 CE1 A:HIS359 4.1 25.5 1.0 O4 A:SO4915 4.1 35.0 1.0 CB A:ASP311 4.1 29.0 1.0 NE2 A:HIS359 4.3 23.8 1.0 O A:HOH1174 4.4 36.8 1.0 CE A:MET361 4.4 21.5 1.0 ZN A:ZN910 4.5 33.0 1.0 OG1 A:THR209 4.6 33.5 1.0 OD1 A:ASP171 4.6 24.4 1.0 O A:ASP311 4.9 29.9 1.0 CA A:ASP311 4.9 27.1 1.0 OD1 A:ASP473 5.0 27.4 1.0

M.Kawaguchi, T.Okabe, S.Okudaira, K.Hama, K.Kano, H.Nishimasu, H.Nakagawa, R.Ishitani, H.Kojima, O.Nureki, J.Aoki, T.Nagano. Identification of Potent in Vivo Autotaxin Inhibitors That Bind to Both Hydrophobic Pocket and Channel in the Catalytic Domain. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32134652
DOI: 10.1021/ACS.JMEDCHEM.9B01967