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Fluorine in PDB 3qro: 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: 3qro 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) 23.47 / 1.62
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.410, 86.280, 46.240, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.3

Other elements in 3qro:

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 3qro). 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: 3qro:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3qro

Go back to Fluorine Binding Sites List in 3qro
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:21.5
occ:1.00
 F35 A:NK9100 0.0 21.5 1.0
C34 A:NK9100 1.3 21.6 1.0
F37 A:NK9100 2.1 24.4 1.0
F36 A:NK9100 2.1 16.1 1.0
C33 A:NK9100 2.3 8.6 1.0
C38 A:NK9100 2.7 11.6 1.0
CZ B:ARG8 3.0 14.8 1.0
NH2 B:ARG8 3.1 15.0 1.0
NH1 B:ARG8 3.1 17.2 1.0
O A:HOH135 3.2 20.0 1.0
NE B:ARG8 3.5 13.2 1.0
C32 A:NK9100 3.6 10.0 1.0
O A:HOH108 3.9 13.1 1.0
O B:HOH122 4.1 39.1 1.0
C39 A:NK9100 4.1 11.1 1.0
CG2 B:VAL82 4.2 16.4 0.2
CD B:ARG8 4.2 13.6 1.0
O B:HOH127 4.4 34.5 1.0
CG1 B:VAL82 4.5 17.2 0.8
OD2 A:ASP29 4.6 15.8 1.0
CG2 B:VAL82 4.7 8.2 0.8
C31 A:NK9100 4.8 8.5 1.0
OD1 A:ASP29 4.8 10.8 1.0
O A:GLY27 4.9 9.1 1.0
C30 A:NK9100 4.9 8.2 1.0
CD2 B:LEU23 5.0 9.1 1.0

Fluorine binding site 2 out of 3 in 3qro

Go back to Fluorine Binding Sites List in 3qro
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:16.1
occ:1.00
 F36 A:NK9100 0.0 16.1 1.0
C34 A:NK9100 1.3 21.6 1.0
F35 A:NK9100 2.1 21.5 1.0
F37 A:NK9100 2.1 24.4 1.0
C33 A:NK9100 2.3 8.6 1.0
C32 A:NK9100 2.9 10.0 1.0
O A:HOH161 3.2 28.9 1.0
O A:HOH108 3.3 13.1 1.0
NH2 B:ARG8 3.4 15.0 1.0
C38 A:NK9100 3.4 11.6 1.0
O B:HOH127 3.6 34.5 1.0
O10 A:NK9100 3.6 10.2 1.0
CZ B:ARG8 4.0 14.8 1.0
O A:HOH155 4.1 27.1 1.0
C9 A:NK9100 4.1 9.6 1.0
OD2 A:ASP29 4.2 15.8 1.0
C31 A:NK9100 4.2 8.5 1.0
O A:HOH135 4.3 20.0 1.0
C11 A:NK9100 4.5 9.2 1.0
O B:HOH122 4.5 39.1 1.0
NH1 B:ARG8 4.5 17.2 1.0
O A:HOH136 4.6 20.1 1.0
O A:HOH142 4.6 21.6 1.0
C39 A:NK9100 4.6 11.1 1.0
NE B:ARG8 4.7 13.2 1.0
CG A:ASP29 4.8 12.7 1.0
O A:GLY48 4.9 11.5 1.0
C30 A:NK9100 4.9 8.2 1.0
C8 A:NK9100 5.0 10.8 1.0

Fluorine binding site 3 out of 3 in 3qro

Go back to Fluorine Binding Sites List in 3qro
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:24.4
occ:1.00
 F37 A:NK9100 0.0 24.4 1.0
C34 A:NK9100 1.3 21.6 1.0
F35 A:NK9100 2.1 21.5 1.0
F36 A:NK9100 2.1 16.1 1.0
C33 A:NK9100 2.1 8.6 1.0
C32 A:NK9100 2.8 10.0 1.0
C38 A:NK9100 3.2 11.6 1.0
CB B:PRO81 3.6 15.1 1.0
O B:HOH122 3.7 39.1 1.0
O A:HOH155 3.7 27.1 1.0
CG2 B:VAL82 3.9 16.4 0.2
C31 A:NK9100 4.1 8.5 1.0
CG B:PRO81 4.1 16.5 1.0
O B:HOH127 4.2 34.5 1.0
CG1 B:VAL82 4.3 17.2 0.8
C39 A:NK9100 4.3 11.1 1.0
NH2 B:ARG8 4.4 15.0 1.0
NH1 B:ARG8 4.4 17.2 1.0
CZ B:ARG8 4.6 14.8 1.0
C30 A:NK9100 4.7 8.2 1.0
CG2 B:VAL82 4.7 8.2 0.8
O A:HOH161 4.7 28.9 1.0
CA B:PRO81 4.8 15.2 1.0
C B:PRO81 4.8 11.9 1.0
O10 A:NK9100 4.9 10.2 1.0
CB B:VAL82 5.0 12.4 0.2

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: Sun Dec 13 11:54:00 2020

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