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Fluorine in PDB 3qbf: 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: 3qbf 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) 27.57 / 1.45
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 58.200, 86.140, 46.490, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 19.9

Other elements in 3qbf:

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 3qbf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 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: 3qbf:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3qbf

Go back to Fluorine Binding Sites List in 3qbf
Fluorine binding site 1 out of 3 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:22.0
occ:1.00
F10 A:JHG100 0.0 22.0 1.0
C9 A:JHG100 1.3 27.7 1.0
F11 A:JHG100 2.1 30.7 1.0
F12 A:JHG100 2.2 26.9 1.0
C8 A:JHG100 2.2 24.4 1.0
OD2 A:ASP30 2.7 29.5 1.0
C7 A:JHG100 2.8 26.1 1.0
N A:ASP30 3.0 8.9 1.0
O A:HOH118 3.1 18.1 1.0
N A:ASP29 3.2 6.6 1.0
CG A:ASP30 3.2 18.6 1.0
C13 A:JHG100 3.3 23.4 1.0
CB A:ASP29 3.4 8.6 1.0
CB A:ASP30 3.4 14.5 1.0
CA A:ASP29 3.6 6.3 1.0
CA A:ASP30 3.7 10.4 1.0
C A:ASP29 3.8 7.8 1.0
C6 A:JHG100 4.1 25.8 1.0
C A:ALA28 4.1 7.1 1.0
CG A:ASP29 4.1 12.7 1.0
OD1 A:ASP30 4.2 23.7 1.0
O A:HOH178 4.2 33.4 1.0
O A:ASP30 4.2 9.1 1.0
OD2 A:ASP29 4.3 16.0 1.0
CA A:ALA28 4.4 7.6 1.0
C A:ASP30 4.4 8.4 1.0
C14 A:JHG100 4.5 21.8 1.0
CB A:ALA28 4.6 8.8 1.0
C5 A:JHG100 4.8 24.1 1.0
O A:ASP29 4.9 10.3 1.0

Fluorine binding site 2 out of 3 in 3qbf

Go back to Fluorine Binding Sites List in 3qbf
Fluorine binding site 2 out of 3 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:30.7
occ:1.00
F11 A:JHG100 0.0 30.7 1.0
C9 A:JHG100 1.3 27.7 1.0
F10 A:JHG100 2.1 22.0 1.0
F12 A:JHG100 2.2 26.9 1.0
C8 A:JHG100 2.3 24.4 1.0
OD2 A:ASP30 2.5 29.5 1.0
C7 A:JHG100 2.8 26.1 1.0
CB A:ASP30 3.1 14.5 1.0
CG A:ASP30 3.2 18.6 1.0
CG2 A:ILE47 3.2 13.8 1.0
C13 A:JHG100 3.4 23.4 1.0
CB A:ILE47 3.6 12.2 1.0
CD1 A:ILE47 3.6 12.8 1.0
CD1 A:LEU76 3.7 7.9 1.0
CG2 A:VAL32 4.1 13.5 1.0
N A:ASP30 4.1 8.9 1.0
CA A:ASP30 4.1 10.4 1.0
C6 A:JHG100 4.1 25.8 1.0
CG1 A:ILE47 4.2 13.0 1.0
OD1 A:ASP30 4.4 23.7 1.0
O A:ASP30 4.5 9.1 1.0
C A:ASP30 4.6 8.4 1.0
C14 A:JHG100 4.6 21.8 1.0
C5 A:JHG100 4.8 24.1 1.0
O A:HOH105 4.9 22.6 1.0
CA A:ILE47 5.0 10.7 1.0

Fluorine binding site 3 out of 3 in 3qbf

Go back to Fluorine Binding Sites List in 3qbf
Fluorine binding site 3 out of 3 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:26.9
occ:1.00
F12 A:JHG100 0.0 26.9 1.0
C9 A:JHG100 1.3 27.7 1.0
F11 A:JHG100 2.2 30.7 1.0
F10 A:JHG100 2.2 22.0 1.0
C8 A:JHG100 2.3 24.4 1.0
C13 A:JHG100 2.7 23.4 1.0
O A:HOH105 3.0 22.6 1.0
OD2 A:ASP30 3.2 29.5 1.0
CB A:ILE47 3.6 12.2 1.0
C7 A:JHG100 3.6 26.1 1.0
CG2 A:ILE47 3.6 13.8 1.0
O A:HOH178 3.9 33.4 1.0
O A:HOH118 3.9 18.1 1.0
C14 A:JHG100 4.1 21.8 1.0
CG A:ASP30 4.3 18.6 1.0
CA A:ILE47 4.4 10.7 1.0
O A:HOH146 4.5 34.0 1.0
N A:GLY48 4.6 12.8 1.0
CG1 A:ILE47 4.7 13.0 1.0
C6 A:JHG100 4.7 25.8 1.0
CD1 A:ILE47 4.7 12.8 1.0
CB A:ASP30 4.7 14.5 1.0
O A:GLY48 4.8 18.0 1.0
CB A:ASP29 4.9 8.6 1.0
OD2 A:ASP29 4.9 16.0 1.0
C5 A:JHG100 4.9 24.1 1.0
C A:ILE47 5.0 10.4 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: Wed Jul 31 21:57:59 2024

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