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Fluorine in PDB 2qnn: Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor

Enzymatic activity of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor

All present enzymatic activity of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor, PDB code: 2qnn was solved by J.Boettcher, A.Blum, A.Heine, W.E.Diederich, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.384, 86.179, 46.290, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.3

Other elements in 2qnn:

The structure of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor (pdb code 2qnn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor, PDB code: 2qnn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 2qnn

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Fluorine binding site 1 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated 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 in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:39.3
occ:0.39
 F6 B:QN12501 0.0 39.3 0.4
F4 B:QN12501 1.1 15.0 0.6
F6 B:QN12501 1.3 15.9 0.6
C10 B:QN12501 1.4 17.8 1.0
F4 B:QN12501 2.2 13.4 0.4
F5 B:QN12501 2.2 11.1 0.4
C37 B:QN12501 2.4 11.9 1.0
F5 B:QN12501 2.5 23.5 0.6
O B:GLY48 2.5 19.6 1.0
C36 B:QN12501 3.0 11.1 1.0
C B:GLY48 3.5 14.0 1.0
C39 B:QN12501 3.5 12.7 1.0
C1 A:GOL2602 3.6 47.4 1.0
C19 B:QN12501 3.8 17.0 1.0
C3 B:QN12501 3.9 15.2 1.0
CA B:GLY49 4.0 18.0 1.0
O2 A:GOL2602 4.0 34.7 1.0
O1 A:GOL2602 4.1 29.1 1.0
N B:GLY49 4.1 16.9 1.0
C2 A:GOL2602 4.2 48.8 1.0
C B:GLY49 4.3 17.7 1.0
O B:HOH3042 4.3 19.1 1.0
O A:HOH3040 4.3 21.4 1.0
C3 A:GOL2602 4.3 39.0 1.0
C35 B:QN12501 4.4 12.3 1.0
CA B:GLY48 4.4 16.8 1.0
O B:GLY49 4.4 16.6 1.0
CG A:PRO81 4.7 19.0 1.0
C38 B:QN12501 4.7 10.1 1.0
NH2 A:ARG8 4.9 18.2 1.0
N B:ILE50 4.9 15.0 1.0

Fluorine binding site 2 out of 12 in 2qnn

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Fluorine binding site 2 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated 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 in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:15.9
occ:0.61
 F6 B:QN12501 0.0 15.9 0.6
F6 B:QN12501 1.3 39.3 0.4
F5 B:QN12501 1.3 11.1 0.4
C10 B:QN12501 1.4 17.8 1.0
F4 B:QN12501 2.1 15.0 0.6
F5 B:QN12501 2.2 23.5 0.6
C37 B:QN12501 2.4 11.9 1.0
F4 B:QN12501 2.6 13.4 0.4
C39 B:QN12501 3.0 12.7 1.0
O B:HOH3042 3.1 19.1 1.0
O B:GLY48 3.3 19.6 1.0
C36 B:QN12501 3.5 11.1 1.0
C3 B:QN12501 3.6 15.2 1.0
O2 A:GOL2602 3.7 34.7 1.0
C19 B:QN12501 3.8 17.0 1.0
NH2 A:ARG8 3.9 18.2 1.0
C1 A:GOL2602 4.2 47.4 1.0
C38 B:QN12501 4.3 10.1 1.0
C2 A:GOL2602 4.3 48.8 1.0
C B:GLY48 4.4 14.0 1.0
C3 A:GOL2602 4.4 39.0 1.0
O B:GLY27 4.6 14.3 1.0
CZ A:ARG8 4.6 20.2 1.0
C35 B:QN12501 4.7 12.3 1.0
O1 A:GOL2602 4.9 29.1 1.0
C4 B:QN12501 4.9 11.3 1.0
N2 B:QN12501 5.0 26.0 1.0

Fluorine binding site 3 out of 12 in 2qnn

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Fluorine binding site 3 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated 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 in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:11.1
occ:0.39
 F5 B:QN12501 0.0 11.1 0.4
F5 B:QN12501 1.3 23.5 0.6
F6 B:QN12501 1.3 15.9 0.6
C10 B:QN12501 1.4 17.8 1.0
F4 B:QN12501 2.2 13.4 0.4
F6 B:QN12501 2.2 39.3 0.4
C37 B:QN12501 2.4 11.9 1.0
F4 B:QN12501 2.6 15.0 0.6
C39 B:QN12501 2.7 12.7 1.0
O B:HOH3042 3.3 19.1 1.0
NH2 A:ARG8 3.3 18.2 1.0
C36 B:QN12501 3.7 11.1 1.0
O2 A:GOL2602 3.7 34.7 1.0
CZ A:ARG8 3.7 20.2 1.0
C3 A:GOL2602 3.9 39.0 1.0
NH1 A:ARG8 3.9 18.6 1.0
C38 B:QN12501 4.1 10.1 1.0
CG1 A:VAL82 4.2 11.2 0.5
C2 A:GOL2602 4.2 48.8 1.0
O3 A:GOL2602 4.4 34.0 1.0
O B:GLY27 4.4 14.3 1.0
C1 A:GOL2602 4.5 47.4 1.0
O B:GLY48 4.5 19.6 1.0
NE A:ARG8 4.6 16.5 1.0
CG2 A:VAL82 4.6 20.2 0.5
C3 B:QN12501 4.7 15.2 1.0
C35 B:QN12501 4.8 12.3 1.0
C19 B:QN12501 4.9 17.0 1.0
CD2 A:LEU23 4.9 18.3 1.0
C34 B:QN12501 5.0 9.6 1.0
CB A:VAL82 5.0 14.9 0.5

Fluorine binding site 4 out of 12 in 2qnn

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Fluorine binding site 4 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated 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 in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:23.5
occ:0.61
 F5 B:QN12501 0.0 23.5 0.6
F4 B:QN12501 1.2 13.4 0.4
F5 B:QN12501 1.3 11.1 0.4
C10 B:QN12501 1.4 17.8 1.0
F6 B:QN12501 2.2 15.9 0.6
F4 B:QN12501 2.2 15.0 0.6
C37 B:QN12501 2.3 11.9 1.0
F6 B:QN12501 2.5 39.3 0.4
C39 B:QN12501 2.9 12.7 1.0
CG1 A:VAL82 3.2 11.2 0.5
C3 A:GOL2602 3.3 39.0 1.0
C36 B:QN12501 3.4 11.1 1.0
CG2 A:VAL82 3.5 20.2 0.5
CB A:VAL82 3.9 14.9 0.5
O3 A:GOL2602 3.9 34.0 1.0
O2 A:GOL2602 4.0 34.7 1.0
NH1 A:ARG8 4.0 18.6 1.0
NH2 A:ARG8 4.0 18.2 1.0
CB A:VAL82 4.0 18.3 0.5
C2 A:GOL2602 4.1 48.8 1.0
CZ A:ARG8 4.2 20.2 1.0
C38 B:QN12501 4.2 10.1 1.0
C1 A:GOL2602 4.3 47.4 1.0
CG A:PRO81 4.4 19.0 1.0
O1 A:GOL2602 4.5 29.1 1.0
CG1 A:VAL82 4.5 22.4 0.5
C35 B:QN12501 4.6 12.3 1.0
O B:HOH3042 4.6 19.1 1.0
CB A:PRO81 4.8 17.6 1.0
CG2 A:VAL82 4.9 20.6 0.5
C34 B:QN12501 4.9 9.6 1.0

Fluorine binding site 5 out of 12 in 2qnn

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Fluorine binding site 5 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated 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 in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:13.4
occ:0.39
 F4 B:QN12501 0.0 13.4 0.4
F5 B:QN12501 1.2 23.5 0.6
C10 B:QN12501 1.4 17.8 1.0
F4 B:QN12501 1.4 15.0 0.6
F5 B:QN12501 2.2 11.1 0.4
F6 B:QN12501 2.2 39.3 0.4
C37 B:QN12501 2.3 11.9 1.0
F6 B:QN12501 2.6 15.9 0.6
C36 B:QN12501 3.0 11.1 1.0
C3 A:GOL2602 3.3 39.0 1.0
CG A:PRO81 3.3 19.0 1.0
C39 B:QN12501 3.4 12.7 1.0
CG1 A:VAL82 3.4 11.2 0.5
O1 A:GOL2602 3.8 29.1 1.0
CG2 A:VAL82 3.8 20.2 0.5
CB A:PRO81 3.8 17.6 1.0
C1 A:GOL2602 3.8 47.4 1.0
C2 A:GOL2602 4.0 48.8 1.0
CB A:VAL82 4.1 14.9 0.5
O3 A:GOL2602 4.2 34.0 1.0
O2 A:GOL2602 4.2 34.7 1.0
CB A:VAL82 4.2 18.3 0.5
C35 B:QN12501 4.3 12.3 1.0
CD A:PRO81 4.5 16.9 1.0
C38 B:QN12501 4.6 10.1 1.0
O B:GLY48 4.6 19.6 1.0
N A:VAL82 4.6 15.6 1.0
O A:HOH3040 4.6 21.4 1.0
C A:PRO81 4.7 16.0 1.0
CA A:PRO81 4.8 15.1 1.0
NH2 A:ARG8 4.9 18.2 1.0
NH1 A:ARG8 4.9 18.6 1.0
C34 B:QN12501 4.9 9.6 1.0

Fluorine binding site 6 out of 12 in 2qnn

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Fluorine binding site 6 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated 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 in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:15.0
occ:0.61
 F4 B:QN12501 0.0 15.0 0.6
F6 B:QN12501 1.1 39.3 0.4
C10 B:QN12501 1.4 17.8 1.0
F4 B:QN12501 1.4 13.4 0.4
F6 B:QN12501 2.1 15.9 0.6
F5 B:QN12501 2.2 23.5 0.6
C37 B:QN12501 2.4 11.9 1.0
F5 B:QN12501 2.6 11.1 0.4
C36 B:QN12501 2.8 11.1 1.0
O B:GLY48 3.2 19.6 1.0
C1 A:GOL2602 3.4 47.4 1.0
O1 A:GOL2602 3.5 29.1 1.0
CG A:PRO81 3.6 19.0 1.0
C39 B:QN12501 3.7 12.7 1.0
O A:HOH3040 3.8 21.4 1.0
C B:GLY48 3.9 14.0 1.0
C3 A:GOL2602 3.9 39.0 1.0
O B:GLY49 4.0 16.6 1.0
C B:GLY49 4.1 17.7 1.0
C2 A:GOL2602 4.1 48.8 1.0
C35 B:QN12501 4.2 12.3 1.0
CA B:GLY49 4.2 18.0 1.0
O2 A:GOL2602 4.2 34.7 1.0
CB A:PRO81 4.3 17.6 1.0
N B:GLY49 4.4 16.9 1.0
N B:ILE50 4.7 15.0 1.0
CG1 A:VAL82 4.7 11.2 0.5
C19 B:QN12501 4.7 17.0 1.0
CA B:GLY48 4.8 16.8 1.0
CD A:PRO81 4.8 16.9 1.0
C38 B:QN12501 4.8 10.1 1.0

Fluorine binding site 7 out of 12 in 2qnn

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Fluorine binding site 7 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:17.3
occ:0.53
 F3 B:QN12501 0.0 17.3 0.5
F3 B:QN12501 1.0 21.9 0.5
C11 B:QN12501 1.4 14.1 1.0
F1 B:QN12501 1.7 14.4 0.5
F2 B:QN12501 2.2 14.1 0.5
F1 B:QN12501 2.2 10.8 0.5
C31 B:QN12501 2.4 10.6 1.0
F2 B:QN12501 2.6 16.9 0.5
C30 B:QN12501 2.7 13.9 1.0
O A:HOH3018 2.9 15.8 1.0
NH2 B:ARG8 3.1 19.2 1.0
CZ B:ARG8 3.1 21.4 1.0
NE B:ARG8 3.5 15.1 1.0
C29 B:QN12501 3.6 10.3 1.0
NH1 B:ARG8 3.7 18.1 1.0
O A:GLY27 4.0 13.9 1.0
C14 B:QN12501 4.0 13.1 1.0
OD2 A:ASP29 4.2 22.4 1.0
CD B:ARG8 4.3 12.0 1.0
OD1 A:ASP29 4.3 12.3 1.0
CD2 B:LEU23 4.6 10.4 1.0
CG A:ASP29 4.6 15.8 1.0
C13 B:QN12501 4.7 8.8 1.0
C12 B:QN12501 4.9 10.3 1.0

Fluorine binding site 8 out of 12 in 2qnn

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Fluorine binding site 8 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:21.9
occ:0.47
 F3 B:QN12501 0.0 21.9 0.5
F3 B:QN12501 1.0 17.3 0.5
C11 B:QN12501 1.3 14.1 1.0
F2 B:QN12501 1.4 14.1 0.5
F1 B:QN12501 2.2 14.4 0.5
F2 B:QN12501 2.2 16.9 0.5
C31 B:QN12501 2.4 10.6 1.0
F1 B:QN12501 2.4 10.8 0.5
C30 B:QN12501 2.7 13.9 1.0
CZ B:ARG8 3.2 21.4 1.0
NH2 B:ARG8 3.3 19.2 1.0
NH1 B:ARG8 3.3 18.1 1.0
NE B:ARG8 3.7 15.1 1.0
C29 B:QN12501 3.7 10.3 1.0
O A:HOH3018 3.9 15.8 1.0
C14 B:QN12501 4.1 13.1 1.0
CD B:ARG8 4.4 12.0 1.0
CG1 B:VAL82 4.4 15.0 1.0
CD2 B:LEU23 4.6 10.4 1.0
O A:GLY27 4.7 13.9 1.0
O B:HOH3089 4.8 29.9 1.0
C13 B:QN12501 4.8 8.8 1.0
OD2 A:ASP29 4.9 22.4 1.0
C12 B:QN12501 5.0 10.3 1.0

Fluorine binding site 9 out of 12 in 2qnn

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Fluorine binding site 9 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:14.1
occ:0.53
 F2 B:QN12501 0.0 14.1 0.5
F2 B:QN12501 1.1 16.9 0.5
C11 B:QN12501 1.3 14.1 1.0
F3 B:QN12501 1.4 21.9 0.5
F3 B:QN12501 2.2 17.3 0.5
F1 B:QN12501 2.3 10.8 0.5
C31 B:QN12501 2.3 10.6 1.0
F1 B:QN12501 2.6 14.4 0.5
C30 B:QN12501 3.0 13.9 1.0
C29 B:QN12501 3.3 10.3 1.0
CB B:PRO81 3.8 15.7 1.0
NH2 B:ARG8 4.0 19.2 1.0
NH1 B:ARG8 4.0 18.1 1.0
CZ B:ARG8 4.1 21.4 1.0
CG B:PRO81 4.3 16.4 1.0
C14 B:QN12501 4.3 13.1 1.0
CG1 B:VAL82 4.3 15.0 1.0
C13 B:QN12501 4.5 8.8 1.0
CB B:VAL82 4.7 12.8 1.0
C B:PRO81 4.7 12.6 1.0
O A:HOH3018 4.8 15.8 1.0
O B:PRO81 4.8 13.9 1.0
C12 B:QN12501 4.9 10.3 1.0
CA B:PRO81 4.9 12.1 1.0
NE B:ARG8 4.9 15.1 1.0

Fluorine binding site 10 out of 12 in 2qnn

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Fluorine binding site 10 out of 12 in the Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Hiv-1 Protease in Complex with A Multiple Decorated Pyrrolidine-Based Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2501

b:16.9
occ:0.47
 F2 B:QN12501 0.0 16.9 0.5
F2 B:QN12501 1.1 14.1 0.5
C11 B:QN12501 1.4 14.1 1.0
F1 B:QN12501 1.6 10.8 0.5
F1 B:QN12501 2.2 14.4 0.5
F3 B:QN12501 2.2 21.9 0.5
C31 B:QN12501 2.3 10.6 1.0
F3 B:QN12501 2.6 17.3 0.5
C29 B:QN12501 2.8 10.3 1.0
C30 B:QN12501 3.4 13.9 1.0
CB B:PRO81 3.7 15.7 1.0
C13 B:QN12501 4.2 8.8 1.0
CG B:PRO81 4.2 16.4 1.0
NH2 B:ARG8 4.2 19.2 1.0
O A:GLY48 4.4 11.4 1.0
C14 B:QN12501 4.6 13.1 1.0
CZ B:ARG8 4.7 21.4 1.0
O A:HOH3018 4.7 15.8 1.0
NH1 B:ARG8 4.7 18.1 1.0
O A:HOH3012 4.8 15.4 1.0
C12 B:QN12501 4.9 10.3 1.0
CA B:PRO81 5.0 12.1 1.0

Reference:

A.Blum, J.Bottcher, A.Heine, G.Klebe, W.E.Diederich. Structure-Guided Design of C2-Symmetric Hiv-1 Protease Inhibitors Based on A Pyrrolidine Scaffold. J.Med.Chem. V. 51 2078 2008.
ISSN: ISSN 0022-2623
PubMed: 18348517
DOI: 10.1021/JM701142S
Page generated: Mon Jul 14 14:12:54 2025

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