Fluorine in PDB 8omj: Hkhk-C in Complex with Cpd 37
Enzymatic activity of Hkhk-C in Complex with Cpd 37
All present enzymatic activity of Hkhk-C in Complex with Cpd 37:
2.7.1.3;
Protein crystallography data
The structure of Hkhk-C in Complex with Cpd 37, PDB code: 8omj
was solved by
A.Pautsch,
R.Ebenhoch,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.90 /
1.98
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
82.433,
83.379,
137.361,
90,
90,
90
|
R / Rfree (%)
|
20.9 /
25.2
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Hkhk-C in Complex with Cpd 37
(pdb code 8omj). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Hkhk-C in Complex with Cpd 37, PDB code: 8omj:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 8omj
Go back to
Fluorine Binding Sites List in 8omj
Fluorine binding site 1 out
of 6 in the Hkhk-C in Complex with Cpd 37
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Hkhk-C in Complex with Cpd 37 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:41.0
occ:1.00
|
F13
|
A:VTM301
|
0.0
|
41.0
|
1.0
|
C9
|
A:VTM301
|
1.3
|
40.1
|
1.0
|
F15
|
A:VTM301
|
2.1
|
39.9
|
1.0
|
F14
|
A:VTM301
|
2.1
|
40.8
|
1.0
|
C6
|
A:VTM301
|
2.4
|
38.2
|
1.0
|
C8
|
A:VTM301
|
2.7
|
37.0
|
1.0
|
O
|
A:HOH521
|
3.3
|
33.2
|
1.0
|
CG2
|
A:VAL250
|
3.4
|
26.0
|
1.0
|
OE2
|
A:GLU227
|
3.5
|
56.3
|
1.0
|
C7
|
A:VTM301
|
3.7
|
37.3
|
1.0
|
CG1
|
A:VAL250
|
3.9
|
27.1
|
1.0
|
C12
|
A:VTM301
|
4.1
|
36.3
|
1.0
|
C11
|
A:VTM301
|
4.2
|
36.8
|
1.0
|
CB
|
A:VAL250
|
4.3
|
26.2
|
1.0
|
CD
|
A:GLU227
|
4.4
|
53.6
|
1.0
|
CB
|
A:GLU227
|
4.5
|
36.1
|
1.0
|
CB
|
A:PRO246
|
4.6
|
21.8
|
1.0
|
C10
|
A:VTM301
|
4.8
|
36.7
|
1.0
|
N18
|
A:VTM301
|
4.9
|
36.7
|
1.0
|
CD
|
A:PRO247
|
4.9
|
23.7
|
1.0
|
O
|
A:HOH476
|
4.9
|
44.3
|
1.0
|
N16
|
A:VTM301
|
4.9
|
36.7
|
1.0
|
C21
|
A:VTM301
|
5.0
|
34.3
|
1.0
|
N19
|
A:VTM301
|
5.0
|
35.0
|
1.0
|
CG
|
A:GLU227
|
5.0
|
43.4
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 8omj
Go back to
Fluorine Binding Sites List in 8omj
Fluorine binding site 2 out
of 6 in the Hkhk-C in Complex with Cpd 37
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Hkhk-C in Complex with Cpd 37 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:40.8
occ:1.00
|
F14
|
A:VTM301
|
0.0
|
40.8
|
1.0
|
C9
|
A:VTM301
|
1.3
|
40.1
|
1.0
|
F13
|
A:VTM301
|
2.1
|
41.0
|
1.0
|
F15
|
A:VTM301
|
2.2
|
39.9
|
1.0
|
C6
|
A:VTM301
|
2.4
|
38.2
|
1.0
|
C11
|
A:VTM301
|
3.0
|
36.8
|
1.0
|
C7
|
A:VTM301
|
3.0
|
37.3
|
1.0
|
CB
|
A:PRO246
|
3.3
|
21.8
|
1.0
|
N18
|
A:VTM301
|
3.4
|
36.7
|
1.0
|
C8
|
A:VTM301
|
3.5
|
37.0
|
1.0
|
CB
|
A:GLU227
|
3.6
|
36.1
|
1.0
|
CA
|
A:GLU227
|
3.8
|
32.7
|
1.0
|
CA
|
A:PRO246
|
3.9
|
21.6
|
1.0
|
OE2
|
A:GLU227
|
4.3
|
56.3
|
1.0
|
CG
|
A:PRO246
|
4.4
|
21.8
|
1.0
|
C10
|
A:VTM301
|
4.4
|
36.7
|
1.0
|
N
|
A:GLU227
|
4.4
|
32.6
|
1.0
|
O
|
A:HOH521
|
4.6
|
33.2
|
1.0
|
N
|
A:PRO246
|
4.6
|
20.4
|
1.0
|
C12
|
A:VTM301
|
4.7
|
36.3
|
1.0
|
CD
|
A:PRO247
|
4.7
|
23.7
|
1.0
|
CD
|
A:GLU227
|
4.7
|
53.6
|
1.0
|
CD
|
A:PRO246
|
4.7
|
19.6
|
1.0
|
CG
|
A:GLU227
|
4.7
|
43.4
|
1.0
|
CB
|
A:ALA244
|
4.9
|
21.6
|
1.0
|
CG2
|
A:VAL250
|
4.9
|
26.0
|
1.0
|
N16
|
A:VTM301
|
5.0
|
36.7
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 8omj
Go back to
Fluorine Binding Sites List in 8omj
Fluorine binding site 3 out
of 6 in the Hkhk-C in Complex with Cpd 37
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Hkhk-C in Complex with Cpd 37 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F301
b:39.9
occ:1.00
|
F15
|
A:VTM301
|
0.0
|
39.9
|
1.0
|
C9
|
A:VTM301
|
1.3
|
40.1
|
1.0
|
F13
|
A:VTM301
|
2.1
|
41.0
|
1.0
|
F14
|
A:VTM301
|
2.2
|
40.8
|
1.0
|
C6
|
A:VTM301
|
2.4
|
38.2
|
1.0
|
C11
|
A:VTM301
|
2.9
|
36.8
|
1.0
|
C7
|
A:VTM301
|
3.0
|
37.3
|
1.0
|
CD
|
A:PRO247
|
3.3
|
23.7
|
1.0
|
N18
|
A:VTM301
|
3.4
|
36.7
|
1.0
|
C8
|
A:VTM301
|
3.4
|
37.0
|
1.0
|
CB
|
A:CYS289
|
3.6
|
26.2
|
1.0
|
SG
|
A:CYS289
|
3.8
|
30.4
|
1.0
|
CG2
|
A:VAL250
|
3.9
|
26.0
|
1.0
|
CG1
|
A:VAL250
|
3.9
|
27.1
|
1.0
|
CB
|
A:PRO246
|
4.0
|
21.8
|
1.0
|
CA
|
A:PRO246
|
4.0
|
21.6
|
1.0
|
CG
|
A:PRO247
|
4.2
|
25.4
|
1.0
|
C10
|
A:VTM301
|
4.3
|
36.7
|
1.0
|
N
|
A:PRO247
|
4.5
|
24.0
|
1.0
|
CB
|
A:VAL250
|
4.5
|
26.2
|
1.0
|
C12
|
A:VTM301
|
4.6
|
36.3
|
1.0
|
C
|
A:PRO246
|
4.8
|
23.1
|
1.0
|
N16
|
A:VTM301
|
4.9
|
36.7
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 8omj
Go back to
Fluorine Binding Sites List in 8omj
Fluorine binding site 4 out
of 6 in the Hkhk-C in Complex with Cpd 37
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Hkhk-C in Complex with Cpd 37 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F303
b:40.4
occ:1.00
|
F13
|
B:VTM303
|
0.0
|
40.4
|
1.0
|
C9
|
B:VTM303
|
1.3
|
39.6
|
1.0
|
F14
|
B:VTM303
|
2.1
|
39.9
|
1.0
|
F15
|
B:VTM303
|
2.1
|
40.0
|
1.0
|
C6
|
B:VTM303
|
2.4
|
38.1
|
1.0
|
C8
|
B:VTM303
|
2.7
|
37.6
|
1.0
|
CG2
|
B:VAL250
|
3.4
|
42.9
|
1.0
|
C7
|
B:VTM303
|
3.7
|
37.2
|
1.0
|
CG
|
B:GLU227
|
3.8
|
47.0
|
1.0
|
C12
|
B:VTM303
|
4.1
|
37.5
|
1.0
|
C11
|
B:VTM303
|
4.3
|
36.9
|
1.0
|
CG1
|
B:VAL250
|
4.3
|
42.0
|
1.0
|
CB
|
B:VAL250
|
4.5
|
42.0
|
1.0
|
O
|
B:HOH499
|
4.5
|
39.0
|
1.0
|
CB
|
B:GLU227
|
4.6
|
39.7
|
1.0
|
CB
|
B:PRO246
|
4.6
|
34.7
|
1.0
|
CD
|
B:PRO247
|
4.8
|
35.0
|
1.0
|
C10
|
B:VTM303
|
4.8
|
36.4
|
1.0
|
N16
|
B:VTM303
|
4.9
|
36.6
|
1.0
|
N18
|
B:VTM303
|
4.9
|
36.7
|
1.0
|
N19
|
B:VTM303
|
4.9
|
39.1
|
1.0
|
CD
|
B:GLU227
|
5.0
|
56.7
|
1.0
|
OE2
|
B:GLU227
|
5.0
|
58.6
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 8omj
Go back to
Fluorine Binding Sites List in 8omj
Fluorine binding site 5 out
of 6 in the Hkhk-C in Complex with Cpd 37
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Hkhk-C in Complex with Cpd 37 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F303
b:39.9
occ:1.00
|
F14
|
B:VTM303
|
0.0
|
39.9
|
1.0
|
C9
|
B:VTM303
|
1.3
|
39.6
|
1.0
|
F13
|
B:VTM303
|
2.1
|
40.4
|
1.0
|
F15
|
B:VTM303
|
2.2
|
40.0
|
1.0
|
C6
|
B:VTM303
|
2.4
|
38.1
|
1.0
|
C7
|
B:VTM303
|
3.1
|
37.2
|
1.0
|
C11
|
B:VTM303
|
3.2
|
36.9
|
1.0
|
CG
|
B:GLU227
|
3.3
|
47.0
|
1.0
|
CB
|
B:GLU227
|
3.3
|
39.7
|
1.0
|
C8
|
B:VTM303
|
3.3
|
37.6
|
1.0
|
CA
|
B:GLU227
|
3.6
|
36.3
|
1.0
|
CB
|
B:PRO246
|
3.6
|
34.7
|
1.0
|
N18
|
B:VTM303
|
3.6
|
36.7
|
1.0
|
O
|
B:HOH445
|
3.9
|
19.3
|
1.0
|
N
|
B:GLU227
|
4.2
|
35.5
|
1.0
|
CA
|
B:PRO246
|
4.3
|
34.3
|
1.0
|
C10
|
B:VTM303
|
4.3
|
36.4
|
1.0
|
CG
|
B:PRO246
|
4.5
|
35.0
|
1.0
|
C12
|
B:VTM303
|
4.5
|
37.5
|
1.0
|
CD
|
B:GLU227
|
4.7
|
56.7
|
1.0
|
C
|
B:GLU227
|
4.8
|
35.8
|
1.0
|
CD
|
B:PRO246
|
4.9
|
33.6
|
1.0
|
N16
|
B:VTM303
|
4.9
|
36.6
|
1.0
|
O
|
B:GLU227
|
4.9
|
36.5
|
1.0
|
N
|
B:PRO246
|
5.0
|
34.0
|
1.0
|
CD
|
B:PRO247
|
5.0
|
35.0
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 8omj
Go back to
Fluorine Binding Sites List in 8omj
Fluorine binding site 6 out
of 6 in the Hkhk-C in Complex with Cpd 37
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Hkhk-C in Complex with Cpd 37 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F303
b:40.0
occ:1.00
|
F15
|
B:VTM303
|
0.0
|
40.0
|
1.0
|
C9
|
B:VTM303
|
1.3
|
39.6
|
1.0
|
F13
|
B:VTM303
|
2.1
|
40.4
|
1.0
|
F14
|
B:VTM303
|
2.2
|
39.9
|
1.0
|
C6
|
B:VTM303
|
2.4
|
38.1
|
1.0
|
C11
|
B:VTM303
|
2.9
|
36.9
|
1.0
|
C7
|
B:VTM303
|
3.0
|
37.2
|
1.0
|
CD
|
B:PRO247
|
3.1
|
35.0
|
1.0
|
N18
|
B:VTM303
|
3.3
|
36.7
|
1.0
|
CB
|
B:PRO246
|
3.5
|
34.7
|
1.0
|
C8
|
B:VTM303
|
3.5
|
37.6
|
1.0
|
CA
|
B:PRO246
|
3.6
|
34.3
|
1.0
|
CG2
|
B:VAL250
|
3.9
|
42.9
|
1.0
|
CG
|
B:PRO247
|
4.1
|
37.0
|
1.0
|
N
|
B:PRO247
|
4.1
|
35.5
|
1.0
|
CB
|
B:CYS289
|
4.2
|
33.1
|
1.0
|
C10
|
B:VTM303
|
4.3
|
36.4
|
1.0
|
C
|
B:PRO246
|
4.4
|
35.0
|
1.0
|
SG
|
B:CYS289
|
4.5
|
36.1
|
1.0
|
O
|
B:HOH499
|
4.6
|
39.0
|
1.0
|
C12
|
B:VTM303
|
4.7
|
37.5
|
1.0
|
N
|
B:PRO246
|
4.7
|
34.0
|
1.0
|
CG
|
B:PRO246
|
4.8
|
35.0
|
1.0
|
CG1
|
B:VAL250
|
4.9
|
42.0
|
1.0
|
N16
|
B:VTM303
|
5.0
|
36.6
|
1.0
|
|
Reference:
N.Heine,
A.Weber,
A.Pautsch,
D.Gottschling,
I.Upheus,
M.Bauer,
R.Ebenhoch,
B.Nosse,
J.Kley.
Discovery of Bi-9787, A Potent Zwitterionic Khk-Inhibitor with Oral Bioavailability To Be Published.
Page generated: Fri Aug 2 21:11:26 2024
|