Fluorine in PDB 6vce: Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand

The structure of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand, PDB code: 6vce was solved by Y.-F.Wang, D.W.Kneller, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.48 / 1.18
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.904, 86.207, 46.090, 90.00, 90.00, 90.00
R / Rfree (%)	13.6 / 15.5

The structure of Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand also contains other interesting chemical elements:

Chlorine	(Cl)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand (pdb code 6vce). 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 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand, PDB code: 6vce:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A 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 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:12.7 occ:0.55 F1 B:G6R201 0.0 12.7 0.6 C33 B:G6R201 1.4 9.9 0.6 CG B:PRO81 2.1 17.5 0.5 C35 B:G6R201 2.3 10.0 0.6 C06 B:G6R201 2.4 8.5 0.6 C A:GLY49 2.8 13.7 1.0 N A:ILE50 2.9 15.8 0.6 N A:ILE50 2.9 14.9 0.5 CD B:PRO81 3.0 17.0 0.5 CA A:GLY49 3.0 24.8 1.0 O A:GLY49 3.2 12.9 1.0 CG B:PRO81 3.2 11.5 0.6 CD B:PRO81 3.3 13.3 0.6 C14 B:G6R201 3.4 10.0 0.5 CA A:ILE50 3.5 13.3 0.6 CB B:PRO81 3.5 13.7 0.6 CB B:PRO81 3.5 15.4 0.5 C34 B:G6R201 3.6 10.0 0.6 CA A:ILE50 3.6 12.5 0.5 C07 B:G6R201 3.6 9.4 0.6 C15 B:G6R201 4.0 11.4 0.5 O A:HOH618 4.1 19.2 0.8 CG1 A:ILE50 4.1 13.6 0.6 C08 B:G6R201 4.1 9.6 0.6 N A:GLY49 4.1 20.2 1.0 C13 B:G6R201 4.2 11.2 0.5 CB A:ILE50 4.2 11.2 0.5 N B:PRO81 4.3 13.1 1.0 CB A:ILE50 4.4 12.8 0.6 O A:GLY48 4.4 12.7 1.0 O10 B:G6R201 4.5 9.3 0.5 CA B:PRO81 4.5 13.5 0.6 CA B:PRO81 4.5 14.0 0.5 O A:HOH692 4.5 25.0 0.6 C12 B:G6R201 4.6 9.7 0.5 C A:ILE50 4.6 10.7 0.6 CG1 A:ILE50 4.6 14.5 0.5 C A:GLY48 4.6 12.9 1.0 O B:HOH306 4.7 12.8 1.0 F2 B:G6R201 4.7 14.1 0.6 O B:HOH416 4.8 24.1 0.5 N B:VAL82 4.9 12.5 1.0 C32 B:G6R201 4.9 9.0 0.6 CG1 B:VAL82 4.9 18.2 0.6 OG1 B:THR80 4.9 12.4 1.0 C A:ILE50 4.9 12.3 0.5 O A:ILE50 4.9 11.5 0.6 O9 B:G6R201 5.0 8.7 0.6

Fluorine binding site 2 out of 4 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A 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 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:12.9 occ:0.45 F1 B:G6R201 0.0 12.9 0.5 C33 B:G6R201 1.3 10.8 0.5 C35 B:G6R201 2.3 11.7 0.5 C06 B:G6R201 2.3 9.9 0.5 C B:GLY49 2.4 13.9 0.6 CA B:GLY49 2.5 19.9 0.6 CG A:PRO81 2.5 12.0 0.6 N B:ILE50 2.6 12.4 0.6 O B:HOH349 3.0 20.2 0.6 O B:GLY49 3.0 12.0 0.6 C B:GLY49 3.1 15.2 0.5 N B:ILE50 3.1 15.3 0.5 CD A:PRO81 3.1 13.2 0.6 CD A:PRO81 3.2 15.1 0.5 CG A:PRO81 3.2 16.0 0.5 CA B:ILE50 3.3 12.1 0.5 C14 B:G6R201 3.4 9.3 0.6 O B:GLY49 3.4 13.7 0.5 C34 B:G6R201 3.6 11.0 0.5 C07 B:G6R201 3.6 9.5 0.5 CA B:GLY49 3.6 22.7 0.5 CA B:ILE50 3.7 10.7 0.6 CB A:PRO81 3.7 15.9 0.5 N B:GLY49 3.8 19.1 0.6 CB A:PRO81 3.9 14.2 0.6 CG1 B:ILE50 4.0 10.8 0.6 C08 B:G6R201 4.1 12.7 0.5 CB B:ILE50 4.1 11.7 0.5 C15 B:G6R201 4.2 10.0 0.6 C13 B:G6R201 4.3 8.2 0.6 N A:PRO81 4.3 12.6 1.0 CB B:ILE50 4.3 10.1 0.6 O B:GLY48 4.3 14.7 0.5 O B:GLY48 4.4 14.6 0.6 N B:GLY49 4.5 23.2 0.5 C B:ILE50 4.5 11.4 0.5 O B:HOH306 4.5 12.8 1.0 C B:GLY48 4.5 15.4 0.6 C12 B:G6R201 4.6 9.3 0.6 O B:HOH406 4.6 22.0 0.6 O10 B:G6R201 4.6 8.5 0.6 CG1 B:ILE50 4.6 14.9 0.5 F2 B:G6R201 4.6 13.7 0.5 O B:HOH316 4.6 22.5 1.0 CA A:PRO81 4.7 13.7 0.5 C B:GLY48 4.7 17.3 0.5 CA A:PRO81 4.7 13.3 0.6 OG1 A:THR80 4.7 11.9 1.0 O B:HOH405 4.8 27.5 1.0 O B:ILE50 4.8 11.5 0.5 N A:VAL82 4.8 12.1 1.0 C32 B:G6R201 4.9 9.5 0.5 C B:ILE50 4.9 11.8 0.6 CG2 A:VAL82 4.9 21.0 1.0 O9 B:G6R201 5.0 8.2 0.5

Fluorine binding site 3 out of 4 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A 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 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:14.1 occ:0.55 F2 B:G6R201 0.0 14.1 0.6 C34 B:G6R201 1.3 10.0 0.6 C08 B:G6R201 2.3 9.6 0.6 C35 B:G6R201 2.4 10.0 0.6 C15 B:G6R201 2.6 11.4 0.5 O B:HOH392 2.7 17.4 0.5 CG2 B:VAL82 3.3 18.0 0.5 NH2 B:ARG8 3.3 13.4 0.6 C11 B:G6R201 3.4 8.0 0.6 NH1 B:ARG8 3.4 16.2 0.6 C33 B:G6R201 3.6 9.9 0.6 C07 B:G6R201 3.6 9.4 0.6 CZ B:ARG8 3.6 13.4 0.6 O B:HOH416 3.7 24.1 0.5 O B:HOH370 3.7 26.1 0.5 O B:HOH341 3.7 23.6 0.6 O A:HOH656 3.8 13.3 0.5 O A:HOH629 3.9 16.1 1.0 C13 B:G6R201 4.0 11.2 0.5 CG1 B:VAL82 4.0 18.2 0.6 C12 B:G6R201 4.0 9.7 0.5 C59 B:G6R201 4.0 8.2 0.6 C06 B:G6R201 4.1 8.5 0.6 CB B:VAL82 4.2 17.7 0.5 O A:HOH602 4.4 19.9 1.0 CB B:VAL82 4.4 16.9 0.6 CG1 B:VAL82 4.5 17.3 0.5 O2 B:G6R201 4.6 8.9 0.6 NE B:ARG8 4.7 16.2 0.6 F1 B:G6R201 4.7 12.7 0.6 O A:GLY27 4.7 11.1 1.0 CD2 B:LEU23 4.7 12.6 1.0 C32 B:G6R201 4.9 9.0 0.6 O A:HOH692 4.9 25.0 0.6 C14 B:G6R201 4.9 10.0 0.5 CG2 B:VAL82 4.9 24.2 0.6 C69 B:G6R201 5.0 8.2 0.6

Fluorine binding site 4 out of 4 in the Hiv-1 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A 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 Wild Type Protease with Grl-026-18A, A Crown-Like Tetrahydropyranotetrahydrofuran with A Bridged Methylene Group As A P2 Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:13.7 occ:0.45 F2 B:G6R201 0.0 13.7 0.5 C34 B:G6R201 1.3 11.0 0.5 C08 B:G6R201 2.3 12.7 0.5 C35 B:G6R201 2.3 11.7 0.5 O B:HOH349 2.3 20.2 0.6 O A:HOH685 2.5 16.3 0.5 C15 B:G6R201 2.6 10.0 0.6 CG2 A:VAL82 3.1 21.0 1.0 C11 B:G6R201 3.3 10.9 0.5 NH1 A:ARG8 3.4 16.4 0.6 NH2 A:ARG8 3.4 16.2 0.6 C33 B:G6R201 3.5 10.8 0.5 CZ A:ARG8 3.6 15.3 0.6 C07 B:G6R201 3.6 9.5 0.5 O B:HOH406 3.6 22.0 0.6 O A:HOH677 3.9 21.3 0.6 O B:HOH363 4.0 14.9 0.6 C12 B:G6R201 4.0 9.3 0.6 C13 B:G6R201 4.0 8.2 0.6 C06 B:G6R201 4.0 9.9 0.5 O B:HOH333 4.0 15.4 1.0 CB A:VAL82 4.1 17.6 1.0 C59 B:G6R201 4.1 9.8 0.5 CG1 A:VAL82 4.4 19.1 1.0 O B:HOH314 4.5 19.6 0.5 NE A:ARG8 4.6 16.0 0.6 O2 B:G6R201 4.6 10.8 0.5 F1 B:G6R201 4.6 12.9 0.5 O B:GLY27 4.7 11.3 1.0 C14 B:G6R201 4.8 9.3 0.6 CD2 A:LEU23 4.8 14.0 1.0 C32 B:G6R201 4.8 9.5 0.5 O B:GLY48 4.9 14.6 0.6 C69 B:G6R201 5.0 10.3 0.5

A.K.Ghosh, A.Grillo, J.Raghavaiah, S.Kovela, M.E.Johnson, D.W.Kneller, Y.F.Wang, S.I.Hattori, N.Higashi-Kuwata, I.T.Weber, H.Mitsuya. Design, Synthesis, and X-Ray Studies of Potent Hiv-1 Protease Inhibitors with P2-Carboxamide Functionalities. Acs Med.Chem.Lett. V. 11 1965 2020.
ISSN: ISSN 1948-5875
PubMed: 33062180
DOI: 10.1021/ACSMEDCHEMLETT.9B00670