Fluorine in PDB 6prf: Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
Enzymatic activity of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
All present enzymatic activity of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A:
3.4.23.16;
Protein crystallography data
The structure of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf
was solved by
D.W.Kneller,
J.Agniswamy,
I.T.Weber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.55 /
1.21
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.565,
60.565,
85.139,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.2 /
19
|
Other elements in 6prf:
The structure of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
(pdb code 6prf). 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 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 6prf
Go back to
Fluorine Binding Sites List in 6prf
Fluorine binding site 1 out
of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:22.1
occ:0.50
|
F1
|
B:7OA101
|
0.0
|
22.1
|
0.5
|
C33
|
B:7OA101
|
1.4
|
14.8
|
0.5
|
O
|
B:HOH287
|
1.4
|
33.6
|
0.5
|
O
|
B:HOH202
|
2.3
|
34.3
|
1.0
|
C35
|
B:7OA101
|
2.3
|
18.0
|
0.5
|
C06
|
B:7OA101
|
2.4
|
14.2
|
0.5
|
C15
|
B:7OA101
|
3.1
|
12.8
|
0.5
|
C11
|
B:7OA101
|
3.2
|
14.2
|
0.5
|
CG2
|
B:VAL82
|
3.5
|
24.3
|
1.0
|
NH2
|
B:ARG8
|
3.5
|
27.9
|
0.5
|
NH1
|
B:ARG8
|
3.6
|
43.0
|
0.5
|
C34
|
B:7OA101
|
3.6
|
14.6
|
0.5
|
C07
|
B:7OA101
|
3.6
|
13.0
|
0.5
|
O
|
B:HOH278
|
3.7
|
45.2
|
1.0
|
O
|
A:HOH234
|
3.8
|
14.9
|
0.5
|
O
|
A:HOH255
|
3.8
|
20.1
|
1.0
|
C59
|
B:7OA101
|
4.0
|
12.9
|
0.5
|
C08
|
B:7OA101
|
4.1
|
15.2
|
0.5
|
C12
|
B:7OA101
|
4.2
|
12.0
|
0.5
|
C13
|
B:7OA101
|
4.3
|
12.2
|
0.5
|
CB
|
B:VAL82
|
4.3
|
19.2
|
1.0
|
CZ
|
B:ARG8
|
4.5
|
35.7
|
0.5
|
O2
|
B:7OA101
|
4.5
|
12.7
|
0.5
|
CZ
|
B:ARG8
|
4.5
|
38.4
|
0.5
|
NE
|
B:ARG8
|
4.5
|
29.7
|
0.5
|
O23
|
B:7OA101
|
4.6
|
12.8
|
0.5
|
F2
|
B:7OA101
|
4.7
|
22.1
|
0.5
|
O
|
A:GLY27
|
4.7
|
12.1
|
1.0
|
NH2
|
B:ARG8
|
4.8
|
32.2
|
0.5
|
CG1
|
B:VAL82
|
4.8
|
26.1
|
1.0
|
C49
|
B:7OA101
|
4.8
|
12.2
|
0.5
|
CD1
|
B:LEU23
|
4.9
|
15.5
|
0.5
|
C32
|
B:7OA101
|
4.9
|
11.5
|
0.5
|
O
|
A:GLY48
|
4.9
|
22.6
|
1.0
|
C21
|
B:7OA101
|
4.9
|
10.5
|
0.5
|
|
Fluorine binding site 2 out
of 4 in 6prf
Go back to
Fluorine Binding Sites List in 6prf
Fluorine binding site 2 out
of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:21.9
occ:0.50
|
F1
|
B:7OA101
|
0.0
|
21.9
|
0.5
|
C33
|
B:7OA101
|
1.4
|
15.4
|
0.5
|
O
|
A:HOH239
|
1.4
|
35.3
|
0.5
|
C06
|
B:7OA101
|
2.3
|
14.8
|
0.5
|
O
|
A:HOH208
|
2.4
|
34.4
|
1.0
|
C35
|
B:7OA101
|
2.4
|
16.6
|
0.5
|
C15
|
B:7OA101
|
3.1
|
12.8
|
0.5
|
C11
|
B:7OA101
|
3.2
|
14.6
|
0.5
|
NH2
|
A:ARG8
|
3.6
|
33.7
|
0.5
|
CG2
|
A:VAL82
|
3.6
|
24.7
|
1.0
|
C34
|
B:7OA101
|
3.6
|
15.2
|
0.5
|
C07
|
B:7OA101
|
3.6
|
12.9
|
0.5
|
O
|
A:HOH280
|
3.6
|
30.6
|
0.5
|
O
|
B:HOH228
|
3.7
|
14.8
|
0.5
|
O
|
A:HOH305
|
3.8
|
45.4
|
1.0
|
O
|
B:HOH249
|
3.8
|
19.1
|
1.0
|
C59
|
B:7OA101
|
4.0
|
12.2
|
0.5
|
C08
|
B:7OA101
|
4.1
|
15.6
|
0.5
|
NH1
|
A:ARG8
|
4.1
|
30.8
|
0.5
|
C12
|
B:7OA101
|
4.2
|
11.8
|
0.5
|
C13
|
B:7OA101
|
4.2
|
11.9
|
0.5
|
O
|
B:HOH297
|
4.3
|
39.4
|
1.0
|
CB
|
A:VAL82
|
4.3
|
18.5
|
1.0
|
O2
|
B:7OA101
|
4.5
|
13.3
|
0.5
|
CZ
|
A:ARG8
|
4.5
|
37.8
|
0.5
|
NE
|
A:ARG8
|
4.6
|
34.7
|
0.5
|
O23
|
B:7OA101
|
4.6
|
12.3
|
0.5
|
O
|
B:GLY27
|
4.7
|
11.7
|
1.0
|
F2
|
B:7OA101
|
4.7
|
23.9
|
0.5
|
CG1
|
A:VAL82
|
4.8
|
27.2
|
1.0
|
C49
|
B:7OA101
|
4.8
|
12.5
|
0.5
|
C32
|
B:7OA101
|
4.9
|
11.7
|
0.5
|
C21
|
B:7OA101
|
4.9
|
10.4
|
0.5
|
CD1
|
A:LEU23
|
4.9
|
13.3
|
0.5
|
O
|
B:GLY48
|
4.9
|
22.7
|
0.5
|
CD2
|
A:LEU23
|
4.9
|
14.8
|
0.5
|
N20
|
B:7OA101
|
5.0
|
11.9
|
0.5
|
|
Fluorine binding site 3 out
of 4 in 6prf
Go back to
Fluorine Binding Sites List in 6prf
Fluorine binding site 3 out
of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:22.1
occ:0.50
|
F2
|
B:7OA101
|
0.0
|
22.1
|
0.5
|
C34
|
B:7OA101
|
1.4
|
14.6
|
0.5
|
C08
|
B:7OA101
|
2.3
|
15.2
|
0.5
|
C35
|
B:7OA101
|
2.3
|
18.0
|
0.5
|
C
|
A:GLY49
|
2.9
|
19.7
|
1.0
|
N
|
A:ILE50
|
3.0
|
19.4
|
0.5
|
N
|
A:ILE50
|
3.0
|
19.0
|
0.5
|
CG
|
B:PRO81
|
3.2
|
31.4
|
1.0
|
CA
|
A:ILE50
|
3.2
|
22.4
|
0.5
|
CD
|
B:PRO81
|
3.2
|
23.6
|
1.0
|
O
|
A:GLY49
|
3.3
|
25.0
|
1.0
|
C14
|
B:7OA101
|
3.4
|
12.1
|
0.5
|
CA
|
A:GLY49
|
3.5
|
23.1
|
1.0
|
CG2
|
A:ILE50
|
3.5
|
24.7
|
0.5
|
C33
|
B:7OA101
|
3.6
|
14.8
|
0.5
|
C07
|
B:7OA101
|
3.6
|
13.0
|
0.5
|
CA
|
A:ILE50
|
3.6
|
18.7
|
0.5
|
CB
|
B:PRO81
|
3.7
|
28.8
|
1.0
|
C15
|
B:7OA101
|
3.9
|
12.8
|
0.5
|
CB
|
A:ILE50
|
3.9
|
25.0
|
0.5
|
CG1
|
A:ILE50
|
4.0
|
16.0
|
0.5
|
C06
|
B:7OA101
|
4.1
|
14.2
|
0.5
|
CB
|
A:ILE50
|
4.2
|
16.9
|
0.5
|
C13
|
B:7OA101
|
4.2
|
12.2
|
0.5
|
N
|
B:PRO81
|
4.3
|
18.9
|
1.0
|
OG1
|
B:THR80
|
4.3
|
15.8
|
1.0
|
N
|
A:GLY49
|
4.4
|
20.4
|
1.0
|
C
|
A:ILE50
|
4.5
|
22.1
|
0.5
|
N
|
B:VAL82
|
4.6
|
14.7
|
1.0
|
CA
|
B:PRO81
|
4.6
|
21.7
|
1.0
|
O
|
A:GLY48
|
4.6
|
22.6
|
1.0
|
C12
|
B:7OA101
|
4.6
|
12.0
|
0.5
|
F1
|
B:7OA101
|
4.7
|
22.1
|
0.5
|
O
|
A:HOH204
|
4.7
|
30.9
|
0.5
|
O22
|
B:7OA101
|
4.8
|
11.3
|
0.5
|
O
|
B:HOH211
|
4.8
|
14.7
|
1.0
|
C
|
A:GLY48
|
4.8
|
19.1
|
1.0
|
O10
|
B:7OA101
|
4.9
|
11.7
|
0.5
|
C32
|
B:7OA101
|
4.9
|
11.5
|
0.5
|
CG2
|
B:VAL82
|
4.9
|
24.3
|
1.0
|
O9
|
B:7OA101
|
4.9
|
10.5
|
0.5
|
CB
|
B:VAL82
|
4.9
|
19.2
|
1.0
|
O
|
A:HOH242
|
5.0
|
31.4
|
0.5
|
|
Fluorine binding site 4 out
of 4 in 6prf
Go back to
Fluorine Binding Sites List in 6prf
Fluorine binding site 4 out
of 4 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A
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 Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F101
b:23.9
occ:0.50
|
F2
|
B:7OA101
|
0.0
|
23.9
|
0.5
|
C34
|
B:7OA101
|
1.3
|
15.2
|
0.5
|
C35
|
B:7OA101
|
2.3
|
16.6
|
0.5
|
C08
|
B:7OA101
|
2.3
|
15.6
|
0.5
|
C
|
B:GLY49
|
3.0
|
19.5
|
1.0
|
N
|
B:ILE50
|
3.0
|
19.1
|
0.5
|
CA
|
B:ILE50
|
3.1
|
23.5
|
0.5
|
N
|
B:ILE50
|
3.1
|
18.2
|
0.5
|
CD
|
A:PRO81
|
3.2
|
23.3
|
1.0
|
CG
|
A:PRO81
|
3.3
|
30.4
|
1.0
|
O
|
B:GLY49
|
3.3
|
24.9
|
1.0
|
C14
|
B:7OA101
|
3.4
|
13.1
|
0.5
|
CA
|
B:GLY49
|
3.5
|
22.9
|
1.0
|
CA
|
B:ILE50
|
3.5
|
17.3
|
0.5
|
C33
|
B:7OA101
|
3.6
|
15.4
|
0.5
|
C07
|
B:7OA101
|
3.6
|
12.9
|
0.5
|
CB
|
A:PRO81
|
3.6
|
27.3
|
1.0
|
CG2
|
B:ILE50
|
3.7
|
26.9
|
0.5
|
C15
|
B:7OA101
|
3.8
|
12.8
|
0.5
|
CB
|
B:ILE50
|
4.0
|
27.6
|
0.5
|
CG1
|
B:ILE50
|
4.1
|
16.1
|
0.5
|
C06
|
B:7OA101
|
4.1
|
14.8
|
0.5
|
CB
|
B:ILE50
|
4.1
|
17.6
|
0.5
|
C13
|
B:7OA101
|
4.2
|
11.9
|
0.5
|
C
|
B:ILE50
|
4.2
|
15.7
|
0.5
|
N
|
A:PRO81
|
4.3
|
18.0
|
1.0
|
OG1
|
A:THR80
|
4.3
|
16.0
|
1.0
|
N
|
B:GLY49
|
4.4
|
20.5
|
1.0
|
N
|
A:VAL82
|
4.5
|
15.2
|
1.0
|
O
|
A:HOH305
|
4.5
|
45.4
|
1.0
|
O
|
B:ILE50
|
4.6
|
25.1
|
0.5
|
CA
|
A:PRO81
|
4.6
|
21.6
|
1.0
|
C12
|
B:7OA101
|
4.6
|
11.8
|
0.5
|
O
|
B:GLY48
|
4.6
|
22.7
|
0.5
|
F1
|
B:7OA101
|
4.7
|
21.9
|
0.5
|
O22
|
B:7OA101
|
4.8
|
11.2
|
0.5
|
O
|
B:GLY48
|
4.8
|
20.9
|
0.5
|
O
|
B:HOH211
|
4.8
|
14.7
|
1.0
|
C32
|
B:7OA101
|
4.8
|
11.7
|
0.5
|
C
|
B:ILE50
|
4.9
|
18.6
|
0.5
|
C
|
B:GLY48
|
4.9
|
20.1
|
0.5
|
O10
|
B:7OA101
|
4.9
|
11.6
|
0.5
|
CB
|
A:VAL82
|
4.9
|
18.5
|
1.0
|
O9
|
B:7OA101
|
4.9
|
10.7
|
0.5
|
CG2
|
A:VAL82
|
5.0
|
24.7
|
1.0
|
C
|
A:PRO81
|
5.0
|
15.4
|
1.0
|
|
Reference:
D.W.Kneller,
J.Agniswamy,
A.K.Ghosh,
I.T.Weber.
Potent Antiviral Hiv-1 Protease Inhibitor Combats Highly Drug Resistant Mutant PR20. Biochem.Biophys.Res.Commun. V. 519 61 2019.
ISSN: ESSN 1090-2104
PubMed: 31474336
DOI: 10.1016/J.BBRC.2019.08.126
Page generated: Fri Aug 2 00:28:20 2024
|