Zinc in PDB 3kn2: Hcv NS3 Protease Domain with Ketoamide Inhibitor

The structure of Hcv NS3 Protease Domain with Ketoamide Inhibitor, PDB code: 3kn2 was solved by L.G.Nair, M.Sannigrahi, P.Pinto, S.Bogen, K.X.Chen, G.Njoroge, A.Prongay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.18 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	224.486, 224.486, 75.465, 90.00, 90.00, 120.00
R / Rfree (%)	20 / 26.4

The binding sites of Zinc atom in the Hcv NS3 Protease Domain with Ketoamide Inhibitor (pdb code 3kn2). 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 Ketoamide Inhibitor, PDB code: 3kn2:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Hcv NS3 Protease Domain with 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 Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn901 b:44.7 occ:1.00 O A:HOH192 1.7 19.3 1.0 SG A:CYS97 2.1 33.3 1.0 SG A:CYS99 2.2 55.3 1.0 SG A:CYS145 2.2 45.3 1.0 CB A:CYS145 3.3 38.8 1.0 CB A:CYS97 3.4 42.0 1.0 CB A:CYS99 3.6 55.4 1.0 N A:THR98 3.7 57.7 1.0 CA A:CYS97 3.8 45.6 1.0 N A:CYS99 4.0 59.3 1.0 C A:CYS97 4.2 52.1 1.0 OG A:SER101 4.3 63.7 1.0 CA A:CYS99 4.3 57.1 1.0 CB A:ALA147 4.3 32.4 1.0 CB A:HIS149 4.3 34.1 1.0 C A:THR98 4.4 62.0 1.0 CD2 A:HIS149 4.7 43.0 1.0 CA A:THR98 4.7 61.7 1.0 CG A:HIS149 4.7 36.3 1.0 CA A:CYS145 4.8 38.1 1.0 O A:THR98 4.9 63.5 1.0 C A:CYS99 5.0 57.2 1.0

Zinc binding site 2 out of 2 in the Hcv NS3 Protease Domain with 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 Ketoamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn902 b:36.8 occ:1.00 SG C:CYS99 2.0 40.9 1.0 SG C:CYS97 2.1 36.2 1.0 SG C:CYS145 2.1 32.1 1.0 O C:HOH191 2.1 11.1 1.0 CB C:CYS145 3.3 30.6 1.0 CB C:CYS97 3.3 32.4 1.0 CB C:CYS99 3.4 38.6 1.0 N C:CYS99 3.5 42.8 1.0 N C:THR98 3.8 40.7 1.0 CA C:CYS97 3.8 36.6 1.0 CA C:CYS99 4.0 42.7 1.0 C C:CYS97 4.2 38.8 1.0 CB C:HIS149 4.3 25.0 1.0 N C:GLY100 4.5 42.9 1.0 CB C:ALA147 4.5 27.9 1.0 C C:THR98 4.6 43.0 1.0 C C:CYS99 4.7 43.5 1.0 CA C:CYS145 4.7 28.7 1.0 CA C:THR98 4.8 41.4 1.0 CG C:HIS149 4.8 27.3 1.0 N C:ALA147 4.9 31.2 1.0 ND1 C:HIS149 4.9 27.7 1.0

L.G.Nair, M.Sannigrahi, S.Bogen, P.Pinto, K.X.Chen, A.Prongay, X.Tong, K.C.Cheng, V.Girijavallabhan, F.George Njoroge. P4 Capped Amides and Lactams As Hcv NS3 Protease Inhibitors with Improved Potency and Dmpk Profile. Bioorg.Med.Chem.Lett. V. 20 567 2010.
ISSN: ISSN 0960-894X
PubMed: 20004570
DOI: 10.1016/J.BMCL.2009.11.094