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Fluorine in PDB 3qrm: Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor

Enzymatic activity of Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor

All present enzymatic activity of Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor, PDB code: 3qrm was solved by I.Lindemann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.70 / 1.73
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.940, 86.030, 46.500, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20

Other elements in 3qrm:

The structure of Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor (pdb code 3qrm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor, PDB code: 3qrm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3qrm

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Fluorine binding site 1 out of 6 in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor


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 (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F100

b:27.9
occ:1.00
 F18 A:NK7100 0.0 27.9 1.0
C17 A:NK7100 1.3 31.3 1.0
F19 A:NK7100 2.1 23.2 1.0
F20 A:NK7100 2.1 31.6 1.0
C16 A:NK7100 2.2 15.8 1.0
C15 A:NK7100 2.7 12.7 1.0
C24 A:NK7100 3.4 11.2 1.0
O A:HOH251 3.6 34.5 1.0
CB B:PRO81 3.6 17.0 1.0
O B:HOH288 3.7 29.7 1.0
C14 A:NK7100 4.1 10.4 1.0
CG B:PRO81 4.1 19.5 1.0
O A:GLY48 4.2 11.3 1.0
NH2 B:ARG8 4.4 16.3 1.0
O B:HOH117 4.4 27.3 1.0
C25 A:NK7100 4.6 9.7 1.0
O A:HOH122 4.7 21.6 1.0
O A:HOH119 4.8 16.4 1.0
C23 A:NK7100 4.8 14.9 1.0
CZ B:ARG8 5.0 19.4 1.0

Fluorine binding site 2 out of 6 in 3qrm

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Fluorine binding site 2 out of 6 in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor


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 (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F100

b:23.2
occ:1.00
 F19 A:NK7100 0.0 23.2 1.0
C17 A:NK7100 1.3 31.3 1.0
F18 A:NK7100 2.1 27.9 1.0
F20 A:NK7100 2.1 31.6 1.0
C16 A:NK7100 2.2 15.8 1.0
O A:HOH119 2.9 16.4 1.0
C15 A:NK7100 3.0 12.7 1.0
C24 A:NK7100 3.2 11.2 1.0
NH2 B:ARG8 3.2 16.3 1.0
OD2 A:ASP29 3.8 17.9 1.0
CZ B:ARG8 3.9 19.4 1.0
O A:HOH132 3.9 18.0 1.0
C14 A:NK7100 4.3 10.4 1.0
O B:HOH288 4.3 29.7 1.0
C25 A:NK7100 4.4 9.7 1.0
NH1 B:ARG8 4.4 16.1 1.0
O A:HOH251 4.5 34.5 1.0
NE B:ARG8 4.5 14.3 1.0
CG A:ASP29 4.6 13.1 1.0
O A:HOH122 4.7 21.6 1.0
F41 A:NK7100 4.7 27.1 1.0
C12 A:NK7100 4.8 16.8 1.0
OD1 A:ASP29 4.8 10.7 1.0
C23 A:NK7100 4.9 14.9 1.0
O A:GLY48 4.9 11.3 1.0
O A:GLY27 5.0 11.8 1.0

Fluorine binding site 3 out of 6 in 3qrm

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Fluorine binding site 3 out of 6 in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor


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 (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F100

b:31.6
occ:1.00
 F20 A:NK7100 0.0 31.6 1.0
C17 A:NK7100 1.3 31.3 1.0
F18 A:NK7100 2.1 27.9 1.0
F19 A:NK7100 2.1 23.2 1.0
C16 A:NK7100 2.3 15.8 1.0
C24 A:NK7100 2.6 11.2 1.0
NH2 B:ARG8 3.4 16.3 1.0
NH1 B:ARG8 3.4 16.1 1.0
O B:HOH288 3.4 29.7 1.0
CZ B:ARG8 3.4 19.4 1.0
C15 A:NK7100 3.5 12.7 1.0
CG1 B:VAL82 3.9 14.3 0.7
C25 A:NK7100 4.0 9.7 1.0
O A:HOH132 4.0 18.0 1.0
CG1 B:VAL82 4.1 12.5 0.3
NE B:ARG8 4.3 14.3 1.0
CB B:PRO81 4.4 17.0 1.0
CG2 B:VAL82 4.4 12.4 0.7
O B:HOH117 4.4 27.3 1.0
O A:HOH119 4.5 16.4 1.0
C14 A:NK7100 4.7 10.4 1.0
CB B:VAL82 4.7 12.6 0.3
CG B:PRO81 4.7 19.5 1.0
CB B:VAL82 4.8 12.6 0.7
C23 A:NK7100 4.9 14.9 1.0

Fluorine binding site 4 out of 6 in 3qrm

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Fluorine binding site 4 out of 6 in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor


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 (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F100

b:19.4
occ:1.00
 F39 A:NK7100 0.0 19.4 1.0
C38 A:NK7100 1.3 32.8 1.0
F40 A:NK7100 2.1 33.0 1.0
F41 A:NK7100 2.2 27.1 1.0
C11 A:NK7100 2.3 17.5 1.0
C10 A:NK7100 2.9 20.6 1.0
N A:ASP30 3.0 8.9 1.0
OD2 A:ASP30 3.1 37.0 1.0
N A:ASP29 3.2 6.4 1.0
O A:HOH119 3.3 16.4 1.0
C12 A:NK7100 3.3 16.8 1.0
CG A:ASP30 3.4 24.9 1.0
CB A:ASP29 3.4 11.9 1.0
CB A:ASP30 3.5 12.8 1.0
CA A:ASP29 3.6 8.4 1.0
C A:ASP29 3.8 12.3 1.0
CA A:ASP30 3.8 7.8 1.0
CG A:ASP29 4.1 13.1 1.0
O A:HOH193 4.1 28.2 1.0
OD2 A:ASP29 4.1 17.9 1.0
C9 A:NK7100 4.1 20.6 1.0
C A:ALA28 4.1 7.6 1.0
OD1 A:ASP30 4.2 24.4 1.0
O A:ASP30 4.3 8.8 1.0
CA A:ALA28 4.5 7.1 1.0
C13 A:NK7100 4.5 14.6 1.0
C A:ASP30 4.5 10.0 1.0
C8 A:NK7100 4.8 23.4 1.0
CB A:ALA28 4.8 8.1 1.0
O A:ASP29 4.9 12.5 1.0

Fluorine binding site 5 out of 6 in 3qrm

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Fluorine binding site 5 out of 6 in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F100

b:33.0
occ:1.00
 F40 A:NK7100 0.0 33.0 1.0
C38 A:NK7100 1.3 32.8 1.0
F39 A:NK7100 2.1 19.4 1.0
F41 A:NK7100 2.1 27.1 1.0
C11 A:NK7100 2.3 17.5 1.0
OD2 A:ASP30 2.8 37.0 1.0
C10 A:NK7100 2.8 20.6 1.0
CG2 A:ILE47 3.2 9.4 1.0
CB A:ASP30 3.3 12.8 1.0
C12 A:NK7100 3.4 16.8 1.0
CG A:ASP30 3.5 24.9 1.0
CD1 A:LEU76 3.6 8.2 1.0
CB A:ILE47 3.7 7.0 1.0
CD1 A:ILE47 3.7 13.2 1.0
C9 A:NK7100 4.1 20.6 1.0
N A:ASP30 4.2 8.9 1.0
CG2 A:VAL32 4.2 13.9 1.0
CA A:ASP30 4.3 7.8 1.0
CG1 A:ILE47 4.3 9.2 1.0
O A:ASP30 4.5 8.8 1.0
C13 A:NK7100 4.6 14.6 1.0
OD1 A:ASP30 4.6 24.4 1.0
C A:ASP30 4.6 10.0 1.0
C8 A:NK7100 4.9 23.4 1.0
O A:HOH122 4.9 21.6 1.0

Fluorine binding site 6 out of 6 in 3qrm

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Fluorine binding site 6 out of 6 in the Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hiv-1 Protease (Mutant Q7K L33I L63I) in Complex with A Three-Armed Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F100

b:27.1
occ:1.00
 F41 A:NK7100 0.0 27.1 1.0
C38 A:NK7100 1.3 32.8 1.0
F40 A:NK7100 2.1 33.0 1.0
F39 A:NK7100 2.2 19.4 1.0
C11 A:NK7100 2.3 17.5 1.0
C12 A:NK7100 2.7 16.8 1.0
O A:HOH122 3.1 21.6 1.0
C10 A:NK7100 3.6 20.6 1.0
CG2 A:ILE47 3.6 9.4 1.0
OD2 A:ASP30 3.6 37.0 1.0
CB A:ILE47 3.7 7.0 1.0
O A:HOH193 3.9 28.2 1.0
O A:HOH119 4.0 16.4 1.0
C13 A:NK7100 4.0 14.6 1.0
CA A:ILE47 4.5 6.9 1.0
CG A:ASP30 4.5 24.9 1.0
C9 A:NK7100 4.7 20.6 1.0
OD2 A:ASP29 4.7 17.9 1.0
N A:GLY48 4.7 10.5 1.0
F19 A:NK7100 4.7 23.2 1.0
CG1 A:ILE47 4.8 9.2 1.0
CD1 A:ILE47 4.8 13.2 1.0
C8 A:NK7100 4.9 23.4 1.0
CB A:ASP30 4.9 12.8 1.0
O A:GLY48 4.9 11.3 1.0
CB A:ASP29 4.9 11.9 1.0

Reference:

I.Lindemann, N.Klee, A.Heine, W.E.Diederich, G.Klebe. Design of A Series of Novel Three-Armed Pyrrolidine-Based Inhibitors For Hiv-1 Protease To Be Published.
Page generated: Mon Jul 14 19:00:06 2025

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