Chlorine in PDB 3phe: Hcv NS5B with A Bound Quinolone Inhibitor

The structure of Hcv NS5B with A Bound Quinolone Inhibitor, PDB code: 3phe was solved by J.R.Somoza, N.To, I.Lehoux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	101.751, 101.972, 251.087, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The structure of Hcv NS5B with A Bound Quinolone Inhibitor also contains other interesting chemical elements:

Fluorine

(F)

4 atoms

The binding sites of Chlorine atom in the Hcv NS5B with A Bound Quinolone Inhibitor (pdb code 3phe). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hcv NS5B with A Bound Quinolone Inhibitor, PDB code: 3phe:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl999 b:21.8 occ:1.00 CL39 A:C9A999 0.0 21.8 1.0 C38 A:C9A999 1.7 31.7 1.0 C40 A:C9A999 2.7 33.4 1.0 C37 A:C9A999 2.7 33.8 1.0 O A:LEU419 3.4 32.1 1.0 CB A:ARG422 3.4 31.3 1.0 N A:MET423 3.5 30.6 1.0 CD2 A:TRP528 3.7 27.5 1.0 CB A:MET423 3.7 31.1 1.0 CA A:MET423 3.9 29.9 1.0 CE2 A:TRP528 3.9 27.9 1.0 CE3 A:TRP528 3.9 26.9 1.0 CG A:TRP528 3.9 28.6 1.0 CD2 A:LEU419 4.0 30.5 1.0 C41 A:C9A999 4.0 33.8 1.0 C36 A:C9A999 4.0 34.4 1.0 C A:ARG422 4.1 31.1 1.0 CD A:ARG422 4.1 30.8 1.0 CA A:LEU419 4.2 33.4 1.0 C A:LEU419 4.2 32.7 1.0 NE1 A:TRP528 4.3 27.4 1.0 CD1 A:TRP528 4.3 26.5 1.0 NH1 A:ARG422 4.3 31.4 1.0 NE A:ARG422 4.4 28.9 1.0 CA A:ARG422 4.4 31.1 1.0 CZ3 A:TRP528 4.4 29.2 1.0 CG A:ARG422 4.4 32.6 1.0 CZ2 A:TRP528 4.4 27.1 1.0 CD1 A:LEU419 4.4 34.6 1.0 CZ A:ARG422 4.5 30.8 1.0 CB A:TRP528 4.5 29.9 1.0 C35 A:C9A999 4.6 35.1 1.0 CH2 A:TRP528 4.6 26.5 1.0 CG A:LEU419 4.6 34.4 1.0 CG A:MET423 4.8 30.9 1.0 CB A:LEU419 4.9 33.4 1.0 O A:ARG422 4.9 30.5 1.0 O A:THR418 4.9 31.4 1.0 N A:ARG422 5.0 30.2 1.0

Chlorine binding site 2 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl998 b:22.3 occ:1.00 CL39 B:C9A998 0.0 22.3 1.0 C38 B:C9A998 1.7 28.8 1.0 C37 B:C9A998 2.7 30.1 1.0 C40 B:C9A998 2.7 30.4 1.0 CB B:ARG422 3.4 26.7 1.0 N B:MET423 3.5 28.4 1.0 O B:LEU419 3.5 31.8 1.0 CD2 B:TRP528 3.7 31.2 1.0 CB B:MET423 3.8 29.1 1.0 CE2 B:TRP528 3.9 31.1 1.0 CA B:MET423 3.9 28.6 1.0 CG B:TRP528 4.0 33.1 1.0 CG B:LEU419 4.0 32.6 1.0 C36 B:C9A998 4.0 31.9 1.0 C41 B:C9A998 4.0 33.9 1.0 CD B:ARG422 4.0 30.9 1.0 CA B:LEU419 4.0 29.8 1.0 CE3 B:TRP528 4.1 30.9 1.0 C B:ARG422 4.1 29.0 1.0 NE B:ARG422 4.2 33.0 1.0 NE1 B:TRP528 4.2 30.9 1.0 CD1 B:TRP528 4.2 30.8 1.0 C B:LEU419 4.2 31.0 1.0 CG B:ARG422 4.3 30.2 1.0 CA B:ARG422 4.4 27.8 1.0 CZ2 B:TRP528 4.4 30.6 1.0 CZ B:ARG422 4.5 30.8 1.0 CB B:LEU419 4.5 31.0 1.0 CZ3 B:TRP528 4.5 31.3 1.0 CB B:TRP528 4.6 34.5 1.0 C35 B:C9A998 4.6 34.4 1.0 CD2 B:LEU419 4.6 33.4 1.0 NH1 B:ARG422 4.6 31.0 1.0 CH2 B:TRP528 4.7 31.0 1.0 N B:ARG422 4.9 27.1 1.0 CG B:MET423 5.0 32.4 1.0 CD1 B:LEU419 5.0 33.0 1.0 O B:ARG422 5.0 27.9 1.0 O B:THR418 5.0 34.3 1.0

Chlorine binding site 3 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl997 b:16.9 occ:1.00 CL39 C:C9A997 0.0 16.9 1.0 C38 C:C9A997 1.7 26.4 1.0 C37 C:C9A997 2.7 27.3 1.0 C40 C:C9A997 2.7 29.2 1.0 CB C:ARG422 3.4 28.1 1.0 O C:LEU419 3.5 29.6 1.0 N C:MET423 3.5 29.9 1.0 CD2 C:TRP528 3.6 24.9 1.0 CB C:MET423 3.8 30.1 1.0 CG C:TRP528 3.8 25.6 1.0 CE2 C:TRP528 3.9 25.4 1.0 CA C:MET423 3.9 30.5 1.0 CE3 C:TRP528 3.9 23.6 1.0 C36 C:C9A997 4.0 29.4 1.0 C41 C:C9A997 4.0 30.9 1.0 C C:ARG422 4.0 29.7 1.0 CG C:LEU419 4.1 33.9 1.0 CA C:LEU419 4.1 29.7 1.0 CD1 C:TRP528 4.2 26.3 1.0 CD C:ARG422 4.2 28.4 1.0 NE1 C:TRP528 4.2 22.6 1.0 C C:LEU419 4.2 29.5 1.0 CA C:ARG422 4.3 29.4 1.0 NE C:ARG422 4.3 27.5 1.0 CZ2 C:TRP528 4.4 21.9 1.0 CZ3 C:TRP528 4.4 21.4 1.0 CG C:ARG422 4.4 29.4 1.0 CB C:TRP528 4.4 30.1 1.0 C35 C:C9A997 4.5 33.0 1.0 CH2 C:TRP528 4.6 20.4 1.0 CZ C:ARG422 4.6 29.1 1.0 CB C:LEU419 4.6 31.6 1.0 NH1 C:ARG422 4.7 27.9 1.0 O C:ARG422 4.8 29.2 1.0 CG C:MET423 4.8 31.0 1.0 CD1 C:LEU419 4.8 32.3 1.0 N C:ARG422 5.0 27.0 1.0

Chlorine binding site 4 out of 4 in the Hcv NS5B with A Bound Quinolone Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hcv NS5B with A Bound Quinolone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl996 b:29.5 occ:1.00 CL39 D:C9A996 0.0 29.5 1.0 C38 D:C9A996 1.7 36.0 1.0 C37 D:C9A996 2.7 36.7 1.0 C40 D:C9A996 2.7 35.6 1.0 O D:LEU419 3.3 33.3 1.0 CB D:ARG422 3.4 30.8 1.0 N D:MET423 3.5 30.4 1.0 CB D:MET423 3.7 32.8 1.0 CD2 D:TRP528 3.7 27.0 1.0 CA D:MET423 3.8 32.6 1.0 CE2 D:TRP528 3.9 26.4 1.0 CA D:LEU419 3.9 31.7 1.0 CE3 D:TRP528 4.0 26.1 1.0 CG D:LEU419 4.0 34.3 1.0 CG D:TRP528 4.0 27.3 1.0 C36 D:C9A996 4.0 38.3 1.0 C41 D:C9A996 4.0 37.7 1.0 C D:ARG422 4.0 31.8 1.0 C D:LEU419 4.0 31.8 1.0 CD D:ARG422 4.2 32.9 1.0 NE1 D:TRP528 4.3 26.8 1.0 CA D:ARG422 4.3 31.6 1.0 CD1 D:TRP528 4.3 27.1 1.0 CZ2 D:TRP528 4.4 26.3 1.0 CZ3 D:TRP528 4.4 27.2 1.0 CG D:ARG422 4.4 32.9 1.0 CD1 D:LEU419 4.4 35.8 1.0 CB D:LEU419 4.4 32.8 1.0 NE D:ARG422 4.5 33.0 1.0 C35 D:C9A996 4.6 37.4 1.0 CH2 D:TRP528 4.6 26.7 1.0 NH1 D:ARG422 4.7 31.4 1.0 CB D:TRP528 4.7 29.7 1.0 CZ D:ARG422 4.7 33.9 1.0 CG D:MET423 4.7 33.8 1.0 O D:ARG422 4.8 29.9 1.0 O D:THR418 4.9 31.1 1.0 N D:ARG422 4.9 29.6 1.0

D.V.Kumar, R.Rai, K.A.Brameld, J.R.Somoza, R.Rajagopalan, J.W.Janc, Y.M.Xia, T.L.Ton, M.B.Shaghafi, H.Hu, I.Lehoux, N.To, W.B.Young, M.J.Green. Quinolones As Hcv NS5B Polymerase Inhibitors. Bioorg.Med.Chem.Lett. V. 21 82 2011.
ISSN: ISSN 0960-894X
PubMed: 21145235
DOI: 10.1016/J.BMCL.2010.11.068