Chlorine in PDB 8cqi: Human Heparanase in Complex with Inhibitor R3794

All present enzymatic activity of Human Heparanase in Complex with Inhibitor R3794:
3.2.1.166;

The structure of Human Heparanase in Complex with Inhibitor R3794, PDB code: 8cqi was solved by E.M.Moran, G.J.Davies, C.Chen, E.V.Nieuwendijk, L.Wu, F.Skoulikopoulou, V.V.Riet, H.S.Overkleeft, Z.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.61 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.769, 71.519, 79.32, 90, 95.27, 90
R / Rfree (%)	19.9 / 25.3

The binding sites of Chlorine atom in the Human Heparanase in Complex with Inhibitor R3794 (pdb code 8cqi). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human Heparanase in Complex with Inhibitor R3794, PDB code: 8cqi:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Human Heparanase in Complex with Inhibitor R3794


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human Heparanase in Complex with Inhibitor R3794 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl610 b:43.4 occ:1.00 O B:HOH117 2.8 33.2 1.0 O A:HOH751 3.2 40.3 1.0 O A:HOH797 3.3 39.5 1.0 N A:ALA388 3.4 38.7 1.0 CA A:GLY387 3.8 35.1 1.0 CD1 B:LEU30 3.9 43.7 1.0 CB B:ASP27 3.9 39.8 1.0 CB B:LEU30 4.1 42.8 1.0 C A:GLY387 4.1 35.5 1.0 CB A:ALA388 4.2 40.1 1.0 CA B:LEU30 4.2 41.7 1.0 N B:LEU30 4.3 47.7 1.0 CA A:ALA388 4.4 39.1 1.0 CG B:LEU30 4.6 41.3 1.0 CG B:ASP27 4.7 43.8 1.0 C B:ASN29 4.7 43.9 1.0 ND2 B:ASN29 4.8 49.6 1.0 O B:ASP27 4.9 44.0 1.0 N A:GLY389 5.0 44.5 1.0

Chlorine binding site 2 out of 3 in the Human Heparanase in Complex with Inhibitor R3794


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human Heparanase in Complex with Inhibitor R3794 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl611 b:53.3 occ:1.00 N A:GLY239 3.5 45.5 1.0 CA A:MET278 3.6 43.3 1.0 CB A:MET278 3.7 43.3 1.0 CA A:ASN238 3.9 48.2 1.0 CB A:ASN238 4.0 52.0 1.0 CG A:MET278 4.1 50.8 1.0 CE A:MET278 4.1 56.6 1.0 N A:MET278 4.1 45.0 1.0 CZ A:PHE236 4.2 62.8 1.0 OG A:SER281 4.2 56.5 1.0 C A:ASN238 4.2 47.7 1.0 O A:HOH796 4.4 41.9 1.0 CA A:GLY239 4.4 50.8 1.0 C A:LYS277 4.6 45.8 1.0 O A:LYS277 4.7 49.1 1.0 CG A:LYS277 4.8 58.7 1.0 C A:MET278 4.9 39.2 1.0 SD A:MET278 4.9 53.0 1.0 CE1 A:PHE236 4.9 61.5 1.0 CE2 A:PHE236 4.9 56.5 1.0 CD A:LYS277 5.0 58.3 1.0

Chlorine binding site 3 out of 3 in the Human Heparanase in Complex with Inhibitor R3794


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human Heparanase in Complex with Inhibitor R3794 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl612 b:66.8 occ:1.00 O A:HOH805 2.7 38.1 1.0 OE1 A:GLN270 2.7 37.6 1.0 N A:GLN270 2.9 40.8 1.0 O A:HIS296 3.2 38.8 1.0 CD A:GLN270 3.5 36.9 1.0 CA A:GLY269 3.5 37.8 1.0 CG A:GLN270 3.5 35.7 1.0 C A:HIS296 3.7 33.8 1.0 C A:GLY269 3.7 39.9 1.0 CB A:GLN270 3.7 38.5 1.0 CA A:GLN270 3.9 39.2 1.0 CB A:HIS296 4.0 34.1 1.0 CA A:HIS297 4.1 35.7 1.0 N A:HIS297 4.1 32.9 1.0 N A:TYR298 4.3 28.8 1.0 CD1 A:TYR298 4.3 34.4 1.0 O A:HOH791 4.4 52.9 1.0 CA A:HIS296 4.5 33.5 1.0 C A:HIS297 4.5 34.7 1.0 O A:HOH818 4.6 58.3 1.0 NE2 A:GLN270 4.8 35.6 1.0 N A:GLY269 4.8 41.0 1.0 O A:GLY269 4.9 43.5 1.0 CE1 A:TYR298 4.9 29.4 1.0

Y.Chen, A.M.C.H.Van Den Nieuwendijk, L.Wu, E.Moran, F.Skoulikopoulou, V.Van Riet, H.S.Overkleeft, G.J.Davies, Z.Armstrong. Molecular Basis For Inhibition of Heparanases and Beta-Glucuronidases By Siastatin B. J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
PubMed: 38118176
DOI: 10.1021/JACS.3C04162