Fluorine in PDB 6dj7: Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand)

The structure of Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand), PDB code: 6dj7 was solved by A.E.Wong-Sam, Y.F.Wang, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.00 / 1.31
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.264, 86.053, 46.252, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 20.5

The structure of Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand) also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand) (pdb code 6dj7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand), PDB code: 6dj7:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:17.3 occ:0.55 F39 B:G10201 0.0 17.3 0.6 C30 B:G10201 1.4 17.4 0.6 C6 B:G10201 2.1 18.4 0.5 F40 B:G10201 2.2 18.9 0.6 O B:GLY48 2.2 25.1 0.6 C31 B:G10201 2.4 16.5 0.6 C29 B:G10201 2.4 19.2 0.6 C12 B:G10201 2.6 20.3 0.5 O23 B:G10201 2.7 15.5 0.6 C21 B:G10201 2.8 15.1 0.6 C24 B:G10201 2.8 15.3 0.6 C5 B:G10201 3.0 19.1 0.5 O10 B:G10201 3.0 21.5 0.5 O22 B:G10201 3.0 21.4 0.6 C7 B:G10201 3.1 19.1 0.5 O B:HOH385 3.2 26.4 0.5 O B:GLY48 3.3 16.8 0.5 C B:GLY48 3.3 18.7 0.5 S8 B:G10201 3.3 17.3 0.5 C34 B:G10201 3.3 17.7 0.6 C35 B:G10201 3.3 17.6 0.6 C B:GLY48 3.4 22.8 0.6 N B:GLY49 3.4 16.8 0.5 N20 B:G10201 3.4 16.4 0.6 C33 B:G10201 3.5 16.8 0.6 N11 B:G10201 3.5 19.5 0.5 O28 B:G10201 3.5 16.8 0.6 CA B:GLY49 3.5 20.9 0.6 C27 B:G10201 3.5 16.9 0.6 C36 B:G10201 3.6 18.8 0.6 C13 B:G10201 3.6 18.5 0.5 O B:HOH324 3.6 23.3 0.5 CA B:GLY49 3.6 18.1 0.5 C38 B:G10201 3.7 16.0 0.6 C37 B:G10201 3.7 17.8 0.6 C15 B:G10201 3.7 20.4 0.5 N B:GLY49 3.9 21.8 0.6 CA B:GLY48 4.0 19.0 0.5 C14 B:G10201 4.1 22.8 0.5 C25 B:G10201 4.2 17.3 0.6 C4 B:G10201 4.3 18.1 0.5 C19 B:G10201 4.4 15.0 0.6 C2 B:G10201 4.4 19.5 0.5 O26 B:G10201 4.4 17.2 0.6 C B:GLY49 4.5 19.3 0.5 CA B:GLY48 4.5 25.0 0.6 N B:GLY48 4.5 26.5 0.6 C32 B:G10201 4.6 16.8 0.6 N B:GLY48 4.6 19.7 0.5 O B:HOH366 4.7 25.4 0.6 C16 B:G10201 4.7 18.7 0.5 O9 B:G10201 4.8 18.4 0.5 O B:GLY27 4.8 18.6 1.0 C3 B:G10201 4.9 18.2 0.5 C B:GLY49 4.9 18.8 0.6 O A:HOH602 4.9 18.2 0.6 N B:ILE50 5.0 16.1 0.5

Fluorine binding site 2 out of 4 in the Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:19.2 occ:0.45 F39 B:G10201 0.0 19.2 0.5 C30 B:G10201 1.3 16.5 0.5 C6 B:G10201 2.0 20.1 0.6 F40 B:G10201 2.2 18.3 0.5 C29 B:G10201 2.3 16.9 0.5 C31 B:G10201 2.3 17.2 0.5 C12 B:G10201 2.6 18.4 0.6 O A:GLY48 2.6 16.5 0.5 O23 B:G10201 2.7 17.2 0.5 C24 B:G10201 2.8 17.6 0.5 C21 B:G10201 2.8 16.6 0.5 C7 B:G10201 2.8 22.2 0.6 O22 B:G10201 2.9 18.8 0.5 C5 B:G10201 2.9 18.4 0.6 O10 B:G10201 2.9 16.7 0.6 O A:GLY48 3.3 20.9 0.6 C35 B:G10201 3.3 18.2 0.5 S8 B:G10201 3.3 15.9 0.6 C36 B:G10201 3.4 18.7 0.5 O28 B:G10201 3.4 15.7 0.5 N11 B:G10201 3.5 15.7 0.6 C34 B:G10201 3.5 15.6 0.5 C27 B:G10201 3.5 17.5 0.5 C A:GLY48 3.5 22.7 0.6 N20 B:G10201 3.5 17.3 0.5 O A:HOH618 3.5 23.8 0.6 C37 B:G10201 3.6 19.4 0.5 C13 B:G10201 3.6 17.1 0.6 N A:GLY49 3.7 19.1 0.6 C A:GLY48 3.7 17.6 0.5 C33 B:G10201 3.7 15.6 0.5 CA A:GLY49 3.8 20.2 0.6 C38 B:G10201 3.8 16.6 0.5 C15 B:G10201 3.8 17.5 0.6 CA A:GLY49 4.0 15.8 0.5 C2 B:G10201 4.1 23.3 0.6 C14 B:G10201 4.1 19.4 0.6 C4 B:G10201 4.2 18.4 0.6 C25 B:G10201 4.2 17.7 0.5 N A:GLY49 4.3 16.2 0.5 O26 B:G10201 4.4 17.1 0.5 C19 B:G10201 4.4 16.3 0.5 CA A:GLY48 4.5 21.9 0.6 C A:GLY49 4.5 19.7 0.6 C3 B:G10201 4.6 20.4 0.6 C32 B:G10201 4.7 16.4 0.5 C16 B:G10201 4.7 16.3 0.6 O9 B:G10201 4.7 18.6 0.6 CA A:GLY48 4.8 19.6 0.5 N A:GLY48 4.8 20.7 0.5 O A:GLY49 5.0 24.4 0.6

Fluorine binding site 3 out of 4 in the Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:18.9 occ:0.55 F40 B:G10201 0.0 18.9 0.6 C30 B:G10201 1.4 17.4 0.6 F39 B:G10201 2.2 17.3 0.6 C29 B:G10201 2.3 19.2 0.6 C31 B:G10201 2.4 16.5 0.6 O B:GLY48 2.4 25.1 0.6 O B:HOH366 2.6 25.4 0.6 O28 B:G10201 2.9 16.8 0.6 C27 B:G10201 3.0 16.9 0.6 C7 B:G10201 3.0 19.1 0.5 C6 B:G10201 3.0 18.4 0.5 CA B:GLY48 3.1 19.0 0.5 C B:GLY48 3.2 18.7 0.5 N B:GLY48 3.2 19.7 0.5 O B:HOH357 3.3 25.9 0.5 O B:HOH385 3.4 26.4 0.5 O B:GLY48 3.4 16.8 0.5 O B:HOH324 3.5 23.3 0.5 C B:GLY48 3.5 22.8 0.6 N B:GLY48 3.7 26.5 0.6 C24 B:G10201 3.7 15.3 0.6 N B:GLY49 3.9 16.8 0.5 CA B:GLY48 4.0 25.0 0.6 NH2 A:ARG8 4.1 27.3 0.7 O23 B:G10201 4.1 15.5 0.6 C34 B:G10201 4.2 17.7 0.6 C35 B:G10201 4.2 17.6 0.6 O26 B:G10201 4.3 17.2 0.6 C5 B:G10201 4.4 19.1 0.5 C2 B:G10201 4.4 19.5 0.5 O B:HOH310 4.4 27.5 0.6 C B:ILE47 4.5 23.0 0.5 C12 B:G10201 4.6 20.3 0.5 N B:GLY49 4.6 21.8 0.6 C25 B:G10201 4.7 17.3 0.6 C21 B:G10201 4.7 15.1 0.6 OD2 B:ASP29 4.7 24.0 1.0 O B:HOH382 4.8 29.5 0.5 CA B:GLY49 4.8 18.1 0.5 CA B:GLY49 4.8 20.9 0.6 C B:ILE47 4.8 25.1 0.6 C33 B:G10201 4.8 16.8 0.6 C36 B:G10201 5.0 18.8 0.6 O10 B:G10201 5.0 21.5 0.5

Fluorine binding site 4 out of 4 in the Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hiv-1 Protease with Mutation L76V in Complex with Grl-5010 (Gem- Difluoro-Bis-Tetrahydrofuran As P2 Ligand) within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:18.3 occ:0.45 F40 B:G10201 0.0 18.3 0.5 C30 B:G10201 1.3 16.5 0.5 F39 B:G10201 2.2 19.2 0.5 C31 B:G10201 2.3 17.2 0.5 C29 B:G10201 2.4 16.9 0.5 C7 B:G10201 2.7 22.2 0.6 O A:GLY48 2.7 16.5 0.5 C6 B:G10201 3.0 20.1 0.6 C27 B:G10201 3.0 17.5 0.5 O28 B:G10201 3.1 15.7 0.5 O A:HOH623 3.2 40.7 1.0 O A:GLY48 3.6 20.9 0.6 C A:GLY48 3.6 22.7 0.6 O A:HOH618 3.6 23.8 0.6 C24 B:G10201 3.7 17.6 0.5 CA A:GLY48 3.8 21.9 0.6 O A:HOH678 3.9 38.7 0.5 C A:GLY48 3.9 17.6 0.5 C2 B:G10201 4.0 23.3 0.6 N A:GLY48 4.1 21.1 0.6 N A:GLY48 4.1 20.7 0.5 O23 B:G10201 4.1 17.2 0.5 N A:GLY49 4.2 19.1 0.6 C5 B:G10201 4.3 18.4 0.6 C35 B:G10201 4.3 18.2 0.5 O26 B:G10201 4.4 17.1 0.5 NH1 B:ARG8 4.4 29.7 0.5 C34 B:G10201 4.4 15.6 0.5 N1 B:G10201 4.5 29.6 0.6 CA A:GLY48 4.6 19.6 0.5 C12 B:G10201 4.6 18.4 0.6 C25 B:G10201 4.6 17.7 0.5 C21 B:G10201 4.7 16.6 0.5 O A:HOH604 4.8 36.3 0.6 O22 B:G10201 4.9 18.8 0.5 C36 B:G10201 4.9 18.7 0.5 O10 B:G10201 4.9 16.7 0.6 CA A:GLY49 4.9 20.2 0.6 N A:GLY49 5.0 16.2 0.5 OD2 A:ASP29 5.0 22.4 1.0

A.Wong-Sam, Y.F.Wang, Y.Zhang, A.K.Ghosh, R.W.Harrison, I.T.Weber. Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of Hiv-1 Protease. Acs Omega V. 3 12132 2018.
ISSN: ESSN 2470-1343
PubMed: 30288468
DOI: 10.1021/ACSOMEGA.8B01683