Chlorine in PDB 3gnw: Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C

All present enzymatic activity of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C:
2.7.7.48;

The structure of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C, PDB code: 3gnw was solved by O.Nyanguile, H.De Bondt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	75.59 / 2.39
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	106.534, 107.573, 133.657, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 21.7

The structure of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C (pdb code 3gnw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C, PDB code: 3gnw:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl580 b:34.0 occ:1.00 NE A:ARG501 3.2 29.5 1.0 NE A:ARG505 3.3 40.9 1.0 CD2 A:HIS502 3.6 23.2 1.0 CD A:ARG501 3.6 23.3 1.0 CG A:ARG501 3.7 21.0 1.0 NH2 A:ARG505 3.8 40.4 1.0 CZ A:ARG505 3.8 42.0 1.0 NE2 A:HIS502 3.9 23.2 1.0 CD A:ARG505 4.1 32.5 1.0 CZ A:ARG501 4.4 27.7 1.0 NH1 A:ARG501 4.6 24.3 1.0 CB A:ARG501 4.7 19.7 1.0 NH1 A:ARG505 4.8 43.4 1.0 CG A:HIS502 4.9 23.9 1.0

Chlorine binding site 2 out of 3 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl581 b:25.0 occ:1.00 O A:HOH813 3.1 21.3 1.0 O A:HOH818 3.2 22.0 1.0 O A:HOH612 3.2 9.4 1.0 ND2 A:ASN411 3.3 22.4 1.0 NH1 A:ARG394 3.6 22.6 1.0 CD A:ARG394 3.8 24.3 1.0 OD1 A:ASN411 4.0 25.0 1.0 CG A:ASN411 4.1 25.7 1.0 CA A:PRO391 4.2 23.6 1.0 N A:PRO391 4.2 22.7 1.0 CG A:PRO391 4.2 22.9 1.0 NH1 A:ARG386 4.3 24.3 1.0 CB A:SER407 4.3 27.0 1.0 C37 A:XNC579 4.3 13.3 1.0 CD A:PRO391 4.4 23.8 1.0 CG2 A:THR390 4.4 23.9 1.0 C15 A:XNC579 4.4 15.0 1.0 CZ A:ARG394 4.5 23.7 1.0 OG A:SER407 4.5 27.6 1.0 NE A:ARG394 4.5 25.9 1.0 CB A:PRO391 4.6 23.6 1.0 C A:THR390 4.7 22.6 1.0 O A:HOH678 4.7 11.4 1.0 O A:THR390 4.8 21.8 1.0 CG A:ARG394 4.9 21.9 1.0 O A:HOH664 4.9 17.8 1.0 CB A:THR390 5.0 23.8 1.0

Chlorine binding site 3 out of 3 in the Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hcv NS5B Polymerase in Complex with 1,5 Benzodiazepine Inhibitor 4C within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl580 b:36.7 occ:1.00 O B:HOH782 3.2 20.2 1.0 O B:HOH646 3.2 21.6 1.0 ND2 B:ASN411 3.2 18.6 1.0 O B:HOH780 3.4 31.2 1.0 NH1 B:ARG394 3.5 27.0 1.0 CD B:ARG394 3.8 23.9 1.0 C37 B:XNC579 4.1 22.1 1.0 CG B:ASN411 4.1 21.9 1.0 CA B:PRO391 4.2 22.2 1.0 OD1 B:ASN411 4.2 24.1 1.0 NH1 B:ARG386 4.2 30.6 1.0 N B:PRO391 4.2 23.0 1.0 C15 B:XNC579 4.2 18.0 1.0 CB B:SER407 4.3 27.1 1.0 CG B:PRO391 4.3 20.9 1.0 CD B:PRO391 4.3 22.6 1.0 CZ B:ARG394 4.4 26.6 1.0 CG2 B:THR390 4.5 24.7 1.0 NE B:ARG394 4.5 27.1 1.0 OG B:SER407 4.6 27.4 1.0 CB B:PRO391 4.7 21.1 1.0 C B:THR390 4.8 23.1 1.0 C14 B:XNC579 4.8 19.6 1.0 O B:HOH732 4.8 19.6 1.0 CG B:ARG394 4.9 23.1 1.0 O B:HOH731 4.9 27.1 1.0 CZ B:ARG386 4.9 28.4 1.0 O B:THR390 5.0 23.0 1.0

K.Vandyck, M.D.Cummings, O.Nyanguile, C.W.Boutton, S.Vendeville, D.Mcgowan, B.Devogelaere, K.Amssoms, S.Last, K.Rombauts, A.Tahri, P.Lory, L.Hu, D.A.Beauchamp, K.Simmen, P.Raboisson. Structure-Based Design of A Benzodiazepine Scaffold Yields A Potent Allosteric Inhibitor of Hepatitis C NS5B Rna Polymerase. J.Med.Chem. V. 52 4099 2009.
ISSN: ISSN 0022-2623
PubMed: 19507864
DOI: 10.1021/JM9005548