Zinc in PDB 3knx: Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor

The structure of Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor, PDB code: 3knx was solved by S.Venkatraman, F.Velazquez, W.Wu, M.Blackman, K.X.Chen, S.Bogen, L.Nair, X.Tong, R.Chase, A.Hart, S.Agrawal, J.Pichardo, A.Prongay, K.-C.Cheng, V.Girijavallabhan, J.Piwinski, N.-Y.Shih, F.G.Njoroge, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 2.65
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	223.587, 223.587, 75.282, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 26.3

The binding sites of Zinc atom in the Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor (pdb code 3knx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor, PDB code: 3knx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:46.1 occ:1.00 O A:HOH197 1.5 14.8 1.0 SG A:CYS97 1.9 19.5 1.0 SG A:CYS99 2.3 35.7 1.0 SG A:CYS145 2.3 34.5 1.0 CB A:CYS97 3.3 28.6 1.0 CB A:CYS145 3.3 26.7 1.0 CB A:CYS99 3.5 39.4 1.0 N A:THR98 3.6 46.3 1.0 CA A:CYS97 3.6 35.1 1.0 N A:CYS99 3.8 46.4 1.0 C A:CYS97 4.1 41.8 1.0 CA A:CYS99 4.2 40.6 1.0 CB A:HIS149 4.2 18.2 1.0 CB A:ALA147 4.3 21.3 1.0 C A:THR98 4.3 48.3 1.0 CA A:THR98 4.6 48.9 1.0 O A:HOH259 4.6 51.2 1.0 CG A:HIS149 4.6 24.3 1.0 CD2 A:HIS149 4.8 30.3 1.0 CA A:CYS145 4.8 26.3 1.0 C A:CYS99 4.8 38.9 1.0 N A:GLY100 4.9 37.6 1.0 N A:CYS97 4.9 31.5 1.0

Zinc binding site 2 out of 2 in the Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Hcv NS3 Protease Domain with P1-P3 Macrocyclic Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn902 b:38.7 occ:1.00 O C:HOH190 1.6 2.0 1.0 SG C:CYS145 2.0 22.2 1.0 SG C:CYS97 2.1 22.6 1.0 SG C:CYS99 2.2 23.5 1.0 CB C:CYS145 3.2 26.7 1.0 CB C:CYS99 3.4 23.4 1.0 CB C:CYS97 3.4 20.7 1.0 N C:CYS99 3.7 28.1 1.0 CA C:CYS97 3.9 26.6 1.0 N C:THR98 4.1 34.3 1.0 CA C:CYS99 4.1 26.3 1.0 CB C:HIS149 4.4 10.7 1.0 C C:CYS97 4.4 31.4 1.0 CB C:ALA147 4.5 16.6 1.0 CA C:CYS145 4.6 23.6 1.0 C C:CYS99 4.7 26.8 1.0 N C:GLY100 4.8 26.5 1.0 C C:THR98 4.9 30.8 1.0 CG C:HIS149 4.9 17.3 1.0 N C:ALA147 4.9 21.9 1.0 CD C:PRO146 4.9 21.5 1.0

S.Venkatraman, F.Velazquez, W.Wu, M.Blackman, K.X.Chen, S.Bogen, L.Nair, X.Tong, R.Chase, A.Hart, S.Agrawal, J.Pichardo, A.Prongay, K.C.Cheng, V.Girijavallabhan, J.Piwinski, N.Y.Shih, F.G.Njoroge. Discovery and Structure-Activity Relationship of P1-P3 Ketoamide Derived Macrocyclic Inhibitors of Hepatitis C Virus NS3 Protease. J.Med.Chem. V. 52 336 2009.
ISSN: ISSN 0022-2623
PubMed: 19102654
DOI: 10.1021/JM800940U