Zinc in PDB 4u01: Hcv NS3/4A Serine Protease in Complex with 6570

The structure of Hcv NS3/4A Serine Protease in Complex with 6570, PDB code: 4u01 was solved by C.C.Parsy, F.-R.Alexandre, G.Brandt, C.Caillet, D.Chaves, M.Derock, D.Gloux, Y.Griffon, L.B.Lallos, F.Leroy, M.Liuzzi, A.-G.Loi, B.Mayes, L.Moulat, A.Moussa, M.Chiara, V.Roques, E.Rosinovsky, M.Seifer, A.Stewart, J.Wang, D.Standring, D.Surleraux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.23 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	150.034, 174.363, 133.010, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 29

The structure of Hcv NS3/4A Serine Protease in Complex with 6570 also contains other interesting chemical elements:

Fluorine	(F)	9 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Hcv NS3/4A Serine Protease in Complex with 6570 (pdb code 4u01). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Hcv NS3/4A Serine Protease in Complex with 6570, PDB code: 4u01:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:89.7 occ:1.00 SG A:CYS145 2.2 56.4 1.0 SG A:CYS97 2.2 66.9 1.0 SG A:CYS99 2.8 83.4 1.0 CB A:CYS145 3.2 68.3 1.0 CB A:CYS97 3.3 66.8 1.0 OG A:SER147 3.4 83.6 1.0 CB A:CYS99 3.6 88.1 1.0 CA A:CYS97 3.7 68.1 1.0 N A:CYS99 3.8 84.0 1.0 N A:THR98 4.0 76.5 1.0 CB A:HIS149 4.1 70.8 1.0 CA A:CYS99 4.3 88.4 1.0 C A:CYS97 4.3 72.2 1.0 CG A:HIS149 4.5 74.3 1.0 CB A:SER147 4.6 84.7 1.0 CA A:CYS145 4.7 67.5 1.0 CD2 A:HIS149 4.8 76.4 1.0 C A:THR98 4.9 84.8 1.0 N A:CYS97 4.9 64.2 1.0 N A:SER147 5.0 80.5 1.0 N A:GLY100 5.0 85.4 1.0

Zinc binding site 2 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:0.7 occ:1.00 SG B:CYS97 2.4 1.0 1.0 SG B:CYS99 2.9 0.7 1.0 CB B:CYS97 3.3 0.9 1.0 N B:CYS99 3.3 0.1 1.0 SG B:CYS145 3.3 0.4 1.0 CB B:CYS99 3.3 0.2 1.0 CA B:CYS97 3.4 0.1 1.0 N B:THR98 3.4 0.5 1.0 C B:CYS97 3.8 0.5 1.0 OG B:SER147 3.8 0.1 1.0 CA B:CYS99 3.9 0.3 1.0 C B:THR98 4.3 0.6 1.0 CB B:CYS145 4.3 0.5 1.0 CB B:HIS149 4.4 0.1 1.0 CA B:THR98 4.4 0.3 1.0 N B:GLY100 4.7 0.5 1.0 N B:CYS97 4.7 0.4 1.0 ND1 B:HIS149 4.8 0.7 1.0 C B:CYS99 4.8 0.8 1.0 CG B:HIS149 4.8 0.4 1.0 O B:CYS97 4.9 0.9 1.0

Zinc binding site 3 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn302 b:0.3 occ:1.00 SG C:CYS99 1.8 0.3 1.0 SG C:CYS145 2.2 0.3 1.0 SG C:CYS97 2.3 0.8 1.0 CB C:CYS145 3.0 0.3 1.0 CB C:CYS99 3.2 0.2 1.0 CB C:CYS97 3.2 0.7 1.0 N C:CYS99 3.8 0.8 1.0 CA C:CYS97 3.9 0.3 1.0 CA C:CYS99 4.0 0.1 1.0 OG C:SER147 4.2 0.1 1.0 C C:CYS97 4.3 0.6 1.0 N C:THR98 4.4 0.7 1.0 N C:GLY100 4.5 0.4 1.0 CA C:CYS145 4.5 0.3 1.0 CB C:SER101 4.5 1.0 1.0 CB C:HIS149 4.6 0.7 1.0 C C:CYS99 4.7 0.4 1.0 N C:SER101 4.8 0.2 1.0 CD C:PRO146 4.8 0.8 1.0 C C:THR98 4.9 0.5 1.0 C C:CYS145 5.0 0.4 1.0

Zinc binding site 4 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn302 b:87.4 occ:1.00 SG D:CYS97 2.3 93.7 1.0 SG D:CYS145 2.5 86.2 1.0 SG D:CYS99 2.9 0.7 1.0 CB D:CYS97 3.2 85.1 1.0 OG D:SER147 3.5 99.7 1.0 CB D:CYS99 3.6 0.1 1.0 CB D:CYS145 3.7 85.1 1.0 CA D:CYS97 3.7 87.5 1.0 N D:CYS99 3.9 1.0 1.0 N D:THR98 4.0 99.1 1.0 C D:CYS97 4.3 92.8 1.0 CB D:SER147 4.3 0.3 1.0 CB D:HIS149 4.3 82.5 1.0 CA D:CYS99 4.4 0.7 1.0 CG D:HIS149 4.7 88.6 1.0 ND1 D:HIS149 4.7 93.1 1.0 N D:CYS97 5.0 82.8 1.0 C D:THR98 5.0 0.7 1.0

Zinc binding site 5 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn302 b:0.9 occ:1.00 SG E:CYS97 2.0 0.5 1.0 SG E:CYS145 2.5 0.6 1.0 CB E:CYS97 2.9 0.1 1.0 SG E:CYS99 3.2 0.9 1.0 CA E:CYS97 3.4 0.8 1.0 CB E:CYS145 3.5 0.1 1.0 OG E:SER147 3.6 0.4 1.0 CB E:CYS99 3.8 0.9 1.0 CB E:HIS149 4.0 0.8 1.0 N E:CYS99 4.0 0.6 1.0 N E:THR98 4.1 0.1 1.0 C E:CYS97 4.1 0.1 1.0 CG E:HIS149 4.5 0.7 1.0 ND1 E:HIS149 4.5 0.6 1.0 CA E:CYS99 4.5 0.8 1.0 CB E:SER147 4.7 0.3 1.0 N E:CYS97 4.7 0.4 1.0 CA E:CYS145 4.9 0.8 1.0

Zinc binding site 6 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn302 b:93.4 occ:1.00 SG F:CYS97 1.9 76.1 1.0 SG F:CYS145 2.1 75.1 1.0 SG F:CYS99 2.9 91.5 1.0 CB F:CYS97 3.0 72.3 1.0 CB F:CYS145 3.3 72.3 1.0 CA F:CYS97 3.6 76.0 1.0 OG F:SER147 3.8 90.2 1.0 CB F:CYS99 3.8 94.1 1.0 N F:CYS99 3.8 91.0 1.0 N F:THR98 4.0 86.1 1.0 C F:CYS97 4.2 80.9 1.0 CA F:CYS99 4.3 94.2 1.0 CB F:HIS149 4.3 75.1 1.0 N F:GLY100 4.5 86.5 1.0 CA F:CYS145 4.7 70.7 1.0 CG F:HIS149 4.8 81.2 1.0 C F:CYS99 4.8 91.9 1.0 ND1 F:HIS149 4.9 84.8 1.0 C F:THR98 4.9 93.8 1.0 N F:CYS97 5.0 73.2 1.0 CB F:SER147 5.0 91.8 1.0

Zinc binding site 7 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn302 b:0.6 occ:1.00 SG G:CYS97 1.6 0.4 1.0 CB G:CYS97 2.8 0.9 1.0 SG G:CYS99 3.1 0.8 1.0 SG G:CYS145 3.1 0.3 1.0 CA G:CYS97 3.3 0.2 1.0 N G:THR98 3.5 0.9 1.0 C G:CYS97 3.8 0.9 1.0 N G:CYS99 3.8 0.5 1.0 CB G:CYS145 3.9 0.5 1.0 CB G:CYS99 4.0 0.7 1.0 OG G:SER147 4.0 0.1 1.0 CB G:HIS149 4.2 0.9 1.0 CA G:CYS99 4.5 0.3 1.0 N G:CYS97 4.6 0.9 1.0 CA G:THR98 4.6 0.6 1.0 C G:THR98 4.7 0.7 1.0 N G:GLY100 4.8 0.5 1.0 CG G:HIS149 4.8 0.6 1.0 ND1 G:HIS149 4.8 0.8 1.0 O G:CYS97 4.9 0.3 1.0

Zinc binding site 8 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn302 b:0.2 occ:1.00 SG H:CYS97 1.9 99.8 1.0 SG H:CYS99 2.6 0.3 1.0 SG H:CYS145 3.3 91.0 1.0 CB H:CYS97 3.3 95.2 1.0 CB H:CYS99 3.4 0.0 1.0 N H:CYS99 3.5 0.5 1.0 CA H:CYS97 3.7 98.2 1.0 N H:THR98 3.7 0.4 1.0 C H:CYS97 4.0 0.2 1.0 CB H:CYS145 4.0 92.6 1.0 CA H:CYS99 4.0 0.9 1.0 OG H:SER147 4.2 0.1 1.0 C H:THR98 4.4 0.0 1.0 N H:GLY100 4.4 0.2 1.0 CA H:THR98 4.6 0.5 1.0 CB H:HIS149 4.7 95.0 1.0 C H:CYS99 4.8 0.2 1.0 O H:CYS97 4.8 0.7 1.0

Zinc binding site 9 out of 9 in the Hcv NS3/4A Serine Protease in Complex with 6570


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Hcv NS3/4A Serine Protease in Complex with 6570 within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn302 b:1.0 occ:1.00 SG J:CYS97 2.0 0.1 1.0 SG J:CYS99 2.1 0.7 1.0 CB J:CYS145 3.0 0.9 1.0 CB J:SER101 3.1 0.6 1.0 N J:SER101 3.2 0.7 1.0 SG J:CYS145 3.3 0.4 1.0 N J:GLY100 3.6 1.0 1.0 CB J:CYS99 3.6 0.4 1.0 CA J:SER101 3.7 0.1 1.0 CB J:CYS97 3.7 0.7 1.0 CA J:CYS99 4.2 1.0 1.0 C J:CYS99 4.2 0.2 1.0 N J:CYS99 4.2 0.8 1.0 C J:GLY100 4.2 0.5 1.0 OG J:SER101 4.4 0.3 1.0 CA J:GLY100 4.4 0.0 1.0 CA J:CYS145 4.5 0.3 1.0 CD J:PRO146 4.5 0.8 1.0 O J:SER101 4.5 0.0 1.0 C J:SER101 4.6 0.1 1.0 CA J:CYS97 4.8 0.1 1.0 CG1 J:VAL151 5.0 0.2 1.0

C.C.Parsy, F.R.Alexandre, V.Bidau, F.Bonnaterre, G.Brandt, C.Caillet, S.Cappelle, D.Chaves, T.Convard, M.Derock, D.Gloux, Y.Griffon, L.B.Lallos, F.Leroy, M.Liuzzi, A.G.Loi, L.Moulat, M.Chiara, H.Rahali, V.Roques, E.Rosinovsky, S.Savin, M.Seifer, D.Standring, D.Surleraux. Discovery and Structural Diversity of the Hepatitis C Virus NS3/4A Serine Protease Inhibitor Series Leading to Clinical Candidate IDX320. Bioorg.Med.Chem.Lett. V. 25 5427 2015.
ISSN: ESSN 1464-3405
PubMed: 26410074
DOI: 10.1016/J.BMCL.2015.09.009