Chlorine in PDB 7prt: Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678

The structure of Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678, PDB code: 7prt was solved by L.Wu, Z.Armstrong, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.95 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.808, 71.622, 78.739, 90, 94.89, 90
R / Rfree (%)	19.2 / 23.6

The binding sites of Chlorine atom in the Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678 (pdb code 7prt). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678, PDB code: 7prt:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:38.5 occ:1.00 O A:HOH762 3.2 32.8 1.0 O A:HOH724 3.2 34.0 1.0 N A:ALA388 3.3 32.7 1.0 CA A:GLY387 3.6 31.8 1.0 CB B:LEU30 3.9 40.8 1.0 CD1 B:LEU30 4.0 39.4 1.0 C A:GLY387 4.0 33.9 1.0 CB B:ASP27 4.0 32.4 1.0 CB A:ALA388 4.1 36.1 1.0 N B:LEU30 4.2 37.8 1.0 CA B:LEU30 4.2 40.8 1.0 CA A:ALA388 4.3 36.4 1.0 CG B:LEU30 4.5 41.3 1.0 O3 D:Z612 4.7 33.7 1.0 CB B:ASN29 4.8 47.7 1.0 O B:ASP27 4.8 33.3 1.0 C B:ASN29 4.8 41.2 1.0 CG B:ASP27 4.9 37.0 1.0 N A:GLY389 4.9 35.6 1.0 O A:PHE386 5.0 32.4 1.0 N A:GLY387 5.0 30.1 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Heparanase in Complex with Covalent Inhibitor CB678 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:48.3 occ:1.00 N A:GLY239 3.4 41.9 1.0 CA A:MET278 3.6 37.1 1.0 CB A:ASN238 3.8 43.7 1.0 CA A:ASN238 3.8 41.6 1.0 CB A:MET278 3.8 37.8 1.0 OG A:SER281 3.9 50.3 1.0 N A:MET278 4.0 32.5 1.0 CE A:MET278 4.0 50.2 1.0 C A:ASN238 4.1 37.4 1.0 CZ A:PHE236 4.1 56.1 1.0 CG A:MET278 4.2 40.4 1.0 O A:HOH763 4.3 45.5 1.0 CA A:GLY239 4.4 41.8 1.0 C A:LYS277 4.5 35.3 1.0 O A:LYS277 4.6 34.8 1.0 CD A:LYS277 4.8 58.3 1.0 CE1 A:PHE236 4.8 55.0 1.0 C A:MET278 4.9 34.9 1.0 CG A:LYS277 4.9 53.1 1.0 CE2 A:PHE236 5.0 52.1 1.0

C.De Boer, Z.Armstrong, V.A.J.Lit, U.Barash, G.Ruijgrok, I.Boyango, M.M.Weitzenberg, S.P.Schroder, A.J.C.Sarris, N.J.Meeuwenoord, P.Bule, Y.Kayal, N.Ilan, J.D.C.Codee, I.Vlodavsky, H.S.Overkleeft, G.J.Davies, L.Wu. Mechanism-Based Heparanase Inhibitors Reduce Cancer Metastasis in Vivo. Proc.Natl.Acad.Sci.Usa V. 119 67119 2022.
ISSN: ESSN 1091-6490
PubMed: 35881786
DOI: 10.1073/PNAS.2203167119