Chlorine in PDB 2ynh: Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500

All present enzymatic activity of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500:
2.7.7.49; 2.7.7.7; 3.1.13.2; 3.1.26.13;

The structure of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500, PDB code: 2ynh was solved by P.Chong, P.Sebahar, M.Youngman, D.Garrido, H.Zhang, E.L.Stewart, R.T.Nolte, L.Wang, R.G.Ferris, M.Edelstein, K.Weaver, A.Mathis, A.Peat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.40 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	118.987, 154.567, 156.755, 90.00, 90.00, 90.00
R / Rfree (%)	20.673 / 26.24

The structure of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500 also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Chlorine atom in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500 (pdb code 2ynh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500, PDB code: 2ynh:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1560 b:32.2 occ:1.00 CL1 A:EUR1560 0.0 32.2 1.0 C05 A:EUR1560 1.7 29.3 1.0 N04 A:EUR1560 2.7 30.4 1.0 C07 A:EUR1560 2.8 27.9 1.0 N11 A:EUR1560 3.1 24.7 1.0 O A:LEU234 3.1 18.3 1.0 O A:HIS235 3.1 17.3 1.0 C A:HIS235 3.4 18.1 1.0 C09 A:EUR1560 3.5 26.3 1.0 F30 A:EUR1560 3.7 21.8 1.0 C A:LEU234 3.7 18.1 1.0 C03 A:EUR1560 3.8 29.8 1.0 CD2 A:PHE227 3.9 23.1 1.0 N A:PRO236 3.9 18.9 1.0 N08 A:EUR1560 3.9 28.9 1.0 CE2 A:PHE227 4.0 22.9 1.0 CA A:PRO236 4.1 19.1 1.0 CA A:HIS235 4.1 17.9 1.0 N A:HIS235 4.2 18.1 1.0 C12 A:EUR1560 4.3 23.6 1.0 CB A:LEU234 4.3 17.7 1.0 OH A:TYR318 4.3 14.3 1.0 C29 A:EUR1560 4.5 22.0 1.0 CA A:LEU234 4.6 17.9 1.0 O10 A:EUR1560 4.7 25.9 1.0 CD A:PRO236 4.7 19.1 1.0 CG1 A:VAL106 4.8 24.9 1.0 CB A:PRO225 4.8 31.6 1.0 C13 A:EUR1560 4.8 22.6 1.0 CB A:VAL106 4.9 25.4 1.0 CG A:PRO225 4.9 31.9 1.0 C A:PRO236 5.0 19.0 1.0

Chlorine binding site 2 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1560 b:24.4 occ:1.00 CL2 A:EUR1560 0.0 24.4 1.0 C16 A:EUR1560 1.7 22.6 1.0 C18 A:EUR1560 2.6 22.0 1.0 C15 A:EUR1560 2.7 22.5 1.0 O19 A:EUR1560 2.8 21.3 1.0 CD1 A:TYR181 3.5 21.8 1.0 O A:TYR188 3.7 19.1 1.0 C20 A:EUR1560 3.8 20.8 1.0 CE1 A:TYR181 3.8 22.2 1.0 C A:TYR188 3.8 18.8 1.0 CB A:TYR188 3.8 17.9 1.0 N A:GLY190 3.9 23.0 1.0 C29 A:EUR1560 3.9 22.0 1.0 C21 A:EUR1560 4.0 20.7 1.0 CG1 A:VAL179 4.0 26.2 1.0 C14 A:EUR1560 4.0 22.5 1.0 N A:VAL189 4.1 19.4 1.0 C A:VAL189 4.2 21.4 1.0 CA A:GLY190 4.3 24.2 1.0 CA A:TYR188 4.4 18.3 1.0 CA A:VAL189 4.5 20.4 1.0 C13 A:EUR1560 4.5 22.6 1.0 CG2 A:VAL106 4.5 25.5 1.0 CG A:TYR181 4.6 21.3 1.0 O A:VAL179 4.7 23.9 1.0 CG1 A:VAL106 4.7 24.9 1.0 O A:VAL189 4.8 21.7 1.0 C28 A:EUR1560 4.9 20.8 1.0 F30 A:EUR1560 5.0 21.8 1.0

Chlorine binding site 3 out of 3 in the Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Reverse Transcriptase in Complex with Inhibitor GSK500 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1560 b:21.0 occ:1.00 CL3 A:EUR1560 0.0 21.0 1.0 C22 A:EUR1560 1.7 20.7 1.0 C21 A:EUR1560 2.7 20.7 1.0 C24 A:EUR1560 2.7 20.7 1.0 CH2 A:TRP229 3.7 22.3 1.0 CZ3 A:TRP229 3.8 22.3 1.0 C25 A:EUR1560 4.0 20.8 1.0 C20 A:EUR1560 4.0 20.8 1.0 CD2 A:TYR188 4.0 17.5 1.0 CZ2 A:TRP229 4.0 22.1 1.0 CD1 A:LEU100 4.1 13.1 1.0 CD2 A:LEU100 4.1 13.1 1.0 CE3 A:TRP229 4.2 22.5 1.0 CE2 A:TYR188 4.2 17.6 1.0 CB A:PRO95 4.3 16.0 1.0 CE2 A:TRP229 4.3 22.2 1.0 CD2 A:TRP229 4.4 22.6 1.0 C28 A:EUR1560 4.5 20.8 1.0 CD1 A:LEU234 4.5 17.8 1.0 CG A:PRO95 4.6 16.3 1.0 CG A:LEU100 4.7 13.0 1.0 CD2 A:TYR181 4.8 22.1 1.0 CG A:TYR188 4.9 17.6 1.0 CG A:TYR181 4.9 21.3 1.0

P.Chong, P.Sebahar, M.Youngman, D.Garrido, H.Zhang, E.L.Stewart, R.T.Nolte, L.Wang, R.G.Ferris, M.Edelstein, K.Weaver, A.Mathis, A.Peat. Rational Design of Potent Non-Nucleoside Inhibitors of Hiv- 1 Reverse Transcriptase. J.Med.Chem. V. 55 10601 2012.
ISSN: ISSN 0022-2623
PubMed: 23137340
DOI: 10.1021/JM301294G