Fluorine in PDB 6y9h: Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
Enzymatic activity of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2):
3.4.21.5;
Protein crystallography data
The structure of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2), PDB code: 6y9h
was solved by
A.Sandner,
A.Heine,
G.Klebe,
N.Abazi,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
49.64 /
1.48
|
|
Space group
|
C 1 2 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
70.333,
71.29,
72.534,
90,
100.5,
90
|
|
R / Rfree (%)
|
13.8 /
17
|
Other elements in 6y9h:
The structure of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
(pdb code 6y9h). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2), PDB code: 6y9h:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6y9h
Go back to
Fluorine Binding Sites List in 6y9h
Fluorine binding site 1 out
of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F3
b:21.9
occ:0.56
|
F1
|
C:OGZ3
|
0.0
|
21.9
|
0.6
|
|
C20
|
C:OGZ3
|
1.4
|
23.6
|
0.6
|
|
F
|
C:OGZ3
|
2.2
|
24.7
|
0.6
|
|
F2
|
C:OGZ3
|
2.2
|
26.4
|
0.6
|
|
C19
|
C:OGZ3
|
2.4
|
20.2
|
0.6
|
|
HG13
|
H:VAL213
|
2.6
|
15.6
|
1.0
|
|
C21
|
C:OGZ3
|
2.8
|
17.9
|
0.6
|
|
O
|
H:TRP215
|
3.1
|
12.4
|
1.0
|
|
C16
|
C:OGZ3
|
3.2
|
35.3
|
0.4
|
|
C17
|
C:OGZ3
|
3.2
|
35.6
|
0.4
|
|
H
|
H:PHE227
|
3.3
|
12.9
|
1.0
|
|
H
|
H:TRP215
|
3.3
|
13.9
|
1.0
|
|
CG1
|
H:VAL213
|
3.5
|
13.0
|
1.0
|
|
H
|
H:SER214
|
3.5
|
11.8
|
1.0
|
|
C
|
H:TRP215
|
3.5
|
12.6
|
1.0
|
|
O
|
H:PHE227
|
3.5
|
10.8
|
1.0
|
|
HG12
|
H:VAL213
|
3.6
|
15.6
|
1.0
|
|
HA3
|
H:GLY226
|
3.6
|
15.3
|
1.0
|
|
N
|
H:TRP215
|
3.6
|
11.5
|
1.0
|
|
C18
|
C:OGZ3
|
3.7
|
19.4
|
0.6
|
|
HA2
|
H:GLY226
|
3.7
|
15.3
|
1.0
|
|
HB3
|
H:ALA190
|
3.7
|
22.0
|
1.0
|
|
N
|
H:PHE227
|
3.9
|
10.8
|
1.0
|
|
HG11
|
H:VAL213
|
3.9
|
15.6
|
1.0
|
|
HB1
|
H:ALA190
|
3.9
|
22.0
|
1.0
|
|
CA
|
H:TRP215
|
4.0
|
11.7
|
1.0
|
|
CA
|
H:GLY226
|
4.0
|
12.7
|
1.0
|
|
N
|
H:SER214
|
4.0
|
9.8
|
1.0
|
|
HA
|
H:TRP215
|
4.1
|
14.0
|
1.0
|
|
HA
|
H:VAL213
|
4.1
|
12.9
|
1.0
|
|
C15
|
C:OGZ3
|
4.2
|
17.5
|
0.6
|
|
HA3
|
H:GLY216
|
4.2
|
16.9
|
1.0
|
|
N
|
H:GLY216
|
4.2
|
13.1
|
1.0
|
|
CB
|
H:ALA190
|
4.3
|
18.3
|
1.0
|
|
C
|
H:SER214
|
4.3
|
11.7
|
1.0
|
|
C
|
H:GLY226
|
4.4
|
11.7
|
1.0
|
|
C15
|
C:OGZ3
|
4.4
|
35.4
|
0.4
|
|
C18
|
C:OGZ3
|
4.4
|
36.0
|
0.4
|
|
C
|
H:PHE227
|
4.5
|
10.2
|
1.0
|
|
CA
|
H:VAL213
|
4.6
|
10.7
|
1.0
|
|
CB
|
H:VAL213
|
4.6
|
12.2
|
1.0
|
|
C
|
H:VAL213
|
4.6
|
10.6
|
1.0
|
|
CA
|
H:GLY216
|
4.7
|
14.1
|
1.0
|
|
CZ
|
H:TYR228
|
4.7
|
10.9
|
1.0
|
|
H
|
H:GLY216
|
4.7
|
15.8
|
1.0
|
|
CA
|
H:PHE227
|
4.8
|
10.5
|
1.0
|
|
C17
|
C:OGZ3
|
4.8
|
19.6
|
0.6
|
|
CA
|
H:SER214
|
4.8
|
10.1
|
1.0
|
|
OH
|
H:TYR228
|
4.8
|
12.7
|
1.0
|
|
HG22
|
H:VAL213
|
4.8
|
16.0
|
1.0
|
|
OD1
|
H:ASP189
|
4.9
|
14.6
|
1.0
|
|
HH
|
H:TYR228
|
4.9
|
15.2
|
1.0
|
|
HB2
|
H:ALA190
|
4.9
|
22.0
|
1.0
|
|
H
|
H:ALA190
|
4.9
|
17.0
|
1.0
|
|
HA2
|
H:GLY216
|
4.9
|
16.9
|
1.0
|
|
CE2
|
H:TYR228
|
4.9
|
11.4
|
1.0
|
|
CE1
|
H:TYR228
|
5.0
|
11.0
|
1.0
|
|
C16
|
C:OGZ3
|
5.0
|
18.8
|
0.6
|
|
Fluorine binding site 2 out
of 6 in 6y9h
Go back to
Fluorine Binding Sites List in 6y9h
Fluorine binding site 2 out
of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F3
b:36.9
occ:0.44
|
F1
|
C:OGZ3
|
0.0
|
36.9
|
0.4
|
|
C20
|
C:OGZ3
|
1.3
|
36.7
|
0.4
|
|
OE2
|
H:GLU192
|
1.5
|
29.3
|
0.6
|
|
OE1
|
H:GLU192
|
1.7
|
30.0
|
0.6
|
|
CD
|
H:GLU192
|
1.8
|
28.6
|
0.6
|
|
F
|
C:OGZ3
|
2.1
|
37.0
|
0.4
|
|
F2
|
C:OGZ3
|
2.1
|
36.9
|
0.4
|
|
C19
|
C:OGZ3
|
2.4
|
36.0
|
0.4
|
|
C17
|
C:OGZ3
|
2.8
|
19.6
|
0.6
|
|
C21
|
C:OGZ3
|
3.2
|
35.6
|
0.4
|
|
C16
|
C:OGZ3
|
3.2
|
18.8
|
0.6
|
|
C18
|
C:OGZ3
|
3.2
|
36.0
|
0.4
|
|
CG
|
H:GLU192
|
3.3
|
27.5
|
0.6
|
|
H
|
H:GLU192
|
3.4
|
27.4
|
0.4
|
|
H
|
H:GLU192
|
3.4
|
28.9
|
0.6
|
|
SG
|
H:CYS220
|
3.5
|
21.8
|
1.0
|
|
HB2
|
H:GLU192
|
3.5
|
25.9
|
0.4
|
|
HG3
|
H:GLU192
|
3.6
|
33.0
|
0.6
|
|
HG2
|
H:GLU192
|
3.7
|
33.0
|
0.6
|
|
N
|
H:GLU192
|
3.9
|
22.9
|
0.4
|
|
N
|
H:GLU192
|
3.9
|
24.1
|
0.6
|
|
O
|
H:GLY219
|
4.1
|
22.5
|
1.0
|
|
HA
|
H:CYS191
|
4.1
|
24.9
|
1.0
|
|
C18
|
C:OGZ3
|
4.1
|
19.4
|
0.6
|
|
HB2
|
H:GLU192
|
4.1
|
31.1
|
0.6
|
|
H
|
H:GLY219
|
4.2
|
23.6
|
1.0
|
|
HA2
|
H:GLY219
|
4.2
|
24.6
|
1.0
|
|
CB
|
H:GLU192
|
4.2
|
25.9
|
0.6
|
|
C
|
H:GLY219
|
4.3
|
21.1
|
1.0
|
|
CB
|
H:GLU192
|
4.3
|
21.6
|
0.4
|
|
O
|
C:HOH103
|
4.4
|
28.4
|
1.0
|
|
SG
|
H:CYS191
|
4.4
|
21.4
|
1.0
|
|
C15
|
C:OGZ3
|
4.4
|
35.4
|
0.4
|
|
HA
|
H:GLU192
|
4.4
|
26.1
|
0.4
|
|
C17
|
C:OGZ3
|
4.5
|
35.6
|
0.4
|
|
HG3
|
H:GLU146
|
4.5
|
36.1
|
1.0
|
|
CA
|
H:GLU192
|
4.5
|
24.1
|
0.6
|
|
HA
|
H:GLU192
|
4.5
|
29.0
|
0.6
|
|
CA
|
H:GLU192
|
4.5
|
21.8
|
0.4
|
|
C15
|
C:OGZ3
|
4.5
|
17.5
|
0.6
|
|
CA
|
H:GLY219
|
4.6
|
20.4
|
1.0
|
|
HB3
|
H:GLU192
|
4.6
|
25.9
|
0.4
|
|
N
|
H:GLY219
|
4.7
|
19.6
|
1.0
|
|
C
|
H:CYS191
|
4.7
|
22.9
|
1.0
|
|
CA
|
H:CYS191
|
4.8
|
20.7
|
1.0
|
|
C16
|
C:OGZ3
|
4.9
|
35.3
|
0.4
|
|
N
|
H:CYS220
|
4.9
|
19.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6y9h
Go back to
Fluorine Binding Sites List in 6y9h
Fluorine binding site 3 out
of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F3
b:24.7
occ:0.56
|
F
|
C:OGZ3
|
0.0
|
24.7
|
0.6
|
|
C20
|
C:OGZ3
|
1.3
|
23.6
|
0.6
|
|
F2
|
C:OGZ3
|
2.0
|
26.4
|
0.6
|
|
F1
|
C:OGZ3
|
2.2
|
21.9
|
0.6
|
|
C19
|
C:OGZ3
|
2.3
|
20.2
|
0.6
|
|
HA2
|
H:GLY226
|
2.4
|
15.3
|
1.0
|
|
HA3
|
H:GLY216
|
2.7
|
16.9
|
1.0
|
|
HA3
|
H:GLY226
|
2.8
|
15.3
|
1.0
|
|
C18
|
C:OGZ3
|
2.8
|
19.4
|
0.6
|
|
C17
|
C:OGZ3
|
2.9
|
35.6
|
0.4
|
|
O
|
H:HOH403
|
3.0
|
29.6
|
1.0
|
|
CA
|
H:GLY226
|
3.0
|
12.7
|
1.0
|
|
O
|
H:TRP215
|
3.2
|
12.4
|
1.0
|
|
H
|
H:PHE227
|
3.4
|
12.9
|
1.0
|
|
OD1
|
H:ASP189
|
3.5
|
14.6
|
1.0
|
|
CA
|
H:GLY216
|
3.5
|
14.1
|
1.0
|
|
C21
|
C:OGZ3
|
3.5
|
17.9
|
0.6
|
|
C18
|
C:OGZ3
|
3.6
|
36.0
|
0.4
|
|
C
|
H:TRP215
|
3.6
|
12.6
|
1.0
|
|
C16
|
C:OGZ3
|
3.7
|
35.3
|
0.4
|
|
N
|
H:GLY216
|
3.8
|
13.1
|
1.0
|
|
HA2
|
H:GLY216
|
3.8
|
16.9
|
1.0
|
|
N
|
H:PHE227
|
3.9
|
10.8
|
1.0
|
|
C
|
H:GLY226
|
4.0
|
11.7
|
1.0
|
|
N
|
H:GLY226
|
4.1
|
13.0
|
1.0
|
|
OD2
|
H:ASP189
|
4.1
|
16.6
|
1.0
|
|
C17
|
C:OGZ3
|
4.1
|
19.6
|
0.6
|
|
HB3
|
H:ALA190
|
4.1
|
22.0
|
1.0
|
|
CG
|
H:ASP189
|
4.2
|
15.7
|
1.0
|
|
H
|
H:GLY216
|
4.3
|
15.8
|
1.0
|
|
H
|
H:ALA190
|
4.4
|
17.0
|
1.0
|
|
O
|
H:ALA190
|
4.4
|
16.0
|
1.0
|
|
HB1
|
H:ALA190
|
4.5
|
22.0
|
1.0
|
|
H
|
H:GLY226
|
4.5
|
15.6
|
1.0
|
|
HG13
|
H:VAL213
|
4.5
|
15.6
|
1.0
|
|
O
|
H:TYR225
|
4.5
|
14.0
|
1.0
|
|
H
|
H:TRP215
|
4.7
|
13.9
|
1.0
|
|
O
|
H:HOH455
|
4.7
|
14.5
|
1.0
|
|
C15
|
C:OGZ3
|
4.7
|
17.5
|
0.6
|
|
O
|
H:HOH460
|
4.7
|
25.8
|
1.0
|
|
CB
|
H:ALA190
|
4.7
|
18.3
|
1.0
|
|
C
|
H:TYR225
|
4.7
|
12.6
|
1.0
|
|
CA
|
H:TRP215
|
4.8
|
11.7
|
1.0
|
|
C
|
H:GLY216
|
4.8
|
15.5
|
1.0
|
|
HA
|
H:TRP215
|
4.8
|
14.0
|
1.0
|
|
C19
|
C:OGZ3
|
4.8
|
36.0
|
0.4
|
|
C
|
H:ALA190
|
4.8
|
16.3
|
1.0
|
|
C15
|
C:OGZ3
|
4.9
|
35.4
|
0.4
|
|
C16
|
C:OGZ3
|
4.9
|
18.8
|
0.6
|
|
O
|
H:GLY219
|
5.0
|
22.5
|
1.0
|
|
N
|
H:TRP215
|
5.0
|
11.5
|
1.0
|
|
O
|
H:PHE227
|
5.0
|
10.8
|
1.0
|
|
N
|
H:ALA190
|
5.0
|
14.2
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6y9h
Go back to
Fluorine Binding Sites List in 6y9h
Fluorine binding site 4 out
of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F3
b:37.0
occ:0.44
|
F
|
C:OGZ3
|
0.0
|
37.0
|
0.4
|
|
C20
|
C:OGZ3
|
1.3
|
36.7
|
0.4
|
|
F1
|
C:OGZ3
|
2.1
|
36.9
|
0.4
|
|
F2
|
C:OGZ3
|
2.1
|
36.9
|
0.4
|
|
O
|
H:GLY219
|
2.3
|
22.5
|
1.0
|
|
C19
|
C:OGZ3
|
2.3
|
36.0
|
0.4
|
|
H
|
H:GLY219
|
2.4
|
23.6
|
1.0
|
|
C17
|
C:OGZ3
|
2.6
|
19.6
|
0.6
|
|
C18
|
C:OGZ3
|
2.8
|
36.0
|
0.4
|
|
C
|
H:GLY219
|
2.8
|
21.1
|
1.0
|
|
N
|
H:GLY219
|
2.8
|
19.6
|
1.0
|
|
HA2
|
H:GLY219
|
3.0
|
24.6
|
1.0
|
|
CA
|
H:GLY219
|
3.0
|
20.4
|
1.0
|
|
OE2
|
H:GLU192
|
3.2
|
29.3
|
0.6
|
|
C18
|
C:OGZ3
|
3.4
|
19.4
|
0.6
|
|
C16
|
C:OGZ3
|
3.5
|
18.8
|
0.6
|
|
C21
|
C:OGZ3
|
3.6
|
35.6
|
0.4
|
|
O
|
H:GLY216
|
3.6
|
18.6
|
1.0
|
|
OE1
|
H:GLU192
|
3.7
|
30.0
|
0.6
|
|
SG
|
H:CYS220
|
3.7
|
21.8
|
1.0
|
|
C
|
H:GLU217
|
3.8
|
18.5
|
1.0
|
|
C
|
H:GLY216
|
3.8
|
15.5
|
1.0
|
|
CD
|
H:GLU192
|
3.8
|
28.6
|
0.6
|
|
N
|
H:CYS220
|
3.8
|
19.3
|
1.0
|
|
HA
|
H:GLU217
|
3.9
|
19.7
|
1.0
|
|
HA3
|
H:GLY219
|
4.0
|
24.6
|
1.0
|
|
N
|
H:GLU217
|
4.1
|
14.9
|
1.0
|
|
C17
|
C:OGZ3
|
4.1
|
35.6
|
0.4
|
|
CA
|
H:GLU217
|
4.2
|
16.4
|
1.0
|
|
HA3
|
H:GLY216
|
4.2
|
16.9
|
1.0
|
|
HA
|
H:CYS220
|
4.3
|
23.3
|
1.0
|
|
H
|
H:CYS220
|
4.4
|
23.2
|
1.0
|
|
CA
|
H:GLY216
|
4.6
|
14.1
|
1.0
|
|
CA
|
H:CYS220
|
4.6
|
19.4
|
1.0
|
|
H
|
H:GLY216
|
4.6
|
15.8
|
1.0
|
|
H
|
H:GLU217
|
4.6
|
17.9
|
1.0
|
|
N
|
C:DPN1
|
4.6
|
15.1
|
0.6
|
|
HG3
|
H:GLU146
|
4.6
|
36.1
|
1.0
|
|
HA
|
H:CYS191
|
4.6
|
24.9
|
1.0
|
|
O
|
H:HOH403
|
4.7
|
29.6
|
1.0
|
|
O
|
H:GLU217
|
4.7
|
22.6
|
1.0
|
|
C19
|
C:OGZ3
|
4.7
|
20.2
|
0.6
|
|
N
|
C:DPN1
|
4.7
|
37.0
|
0.4
|
|
C15
|
C:OGZ3
|
4.7
|
35.4
|
0.4
|
|
C15
|
C:OGZ3
|
4.8
|
17.5
|
0.6
|
|
CB
|
H:CYS220
|
4.9
|
21.4
|
1.0
|
|
O
|
C:HOH103
|
4.9
|
28.4
|
1.0
|
|
N
|
H:GLY216
|
4.9
|
13.1
|
1.0
|
|
C16
|
C:OGZ3
|
4.9
|
35.3
|
0.4
|
|
Fluorine binding site 5 out
of 6 in 6y9h
Go back to
Fluorine Binding Sites List in 6y9h
Fluorine binding site 5 out
of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F3
b:26.4
occ:0.56
|
F2
|
C:OGZ3
|
0.0
|
26.4
|
0.6
|
|
C20
|
C:OGZ3
|
1.3
|
23.6
|
0.6
|
|
F
|
C:OGZ3
|
2.0
|
24.7
|
0.6
|
|
F1
|
C:OGZ3
|
2.2
|
21.9
|
0.6
|
|
HB3
|
H:ALA190
|
2.3
|
22.0
|
1.0
|
|
C19
|
C:OGZ3
|
2.3
|
20.2
|
0.6
|
|
HB1
|
H:ALA190
|
2.5
|
22.0
|
1.0
|
|
CB
|
H:ALA190
|
2.7
|
18.3
|
1.0
|
|
C17
|
C:OGZ3
|
2.7
|
35.6
|
0.4
|
|
H
|
H:ALA190
|
3.1
|
17.0
|
1.0
|
|
C18
|
C:OGZ3
|
3.1
|
19.4
|
0.6
|
|
C
|
H:ALA190
|
3.2
|
16.3
|
1.0
|
|
OD1
|
H:ASP189
|
3.3
|
14.6
|
1.0
|
|
CA
|
H:ALA190
|
3.3
|
15.4
|
1.0
|
|
C21
|
C:OGZ3
|
3.3
|
17.9
|
0.6
|
|
O
|
H:ALA190
|
3.3
|
16.0
|
1.0
|
|
HG13
|
H:VAL213
|
3.3
|
15.6
|
1.0
|
|
C16
|
C:OGZ3
|
3.4
|
35.3
|
0.4
|
|
N
|
H:ALA190
|
3.5
|
14.2
|
1.0
|
|
HB2
|
H:ALA190
|
3.6
|
22.0
|
1.0
|
|
HA3
|
H:GLY226
|
3.7
|
15.3
|
1.0
|
|
C18
|
C:OGZ3
|
3.8
|
36.0
|
0.4
|
|
HG11
|
H:VAL213
|
3.9
|
15.6
|
1.0
|
|
N
|
H:CYS191
|
3.9
|
18.4
|
1.0
|
|
CG1
|
H:VAL213
|
4.0
|
13.0
|
1.0
|
|
CG
|
H:ASP189
|
4.1
|
15.7
|
1.0
|
|
HA2
|
H:GLY226
|
4.1
|
15.3
|
1.0
|
|
HA
|
H:ALA190
|
4.2
|
18.5
|
1.0
|
|
H
|
H:CYS191
|
4.3
|
22.1
|
1.0
|
|
HA
|
H:CYS191
|
4.3
|
24.9
|
1.0
|
|
O
|
H:HOH403
|
4.3
|
29.6
|
1.0
|
|
C17
|
C:OGZ3
|
4.4
|
19.6
|
0.6
|
|
CA
|
H:GLY226
|
4.4
|
12.7
|
1.0
|
|
HG12
|
H:VAL213
|
4.4
|
15.6
|
1.0
|
|
HH
|
H:TYR228
|
4.4
|
15.2
|
1.0
|
|
OD2
|
H:ASP189
|
4.4
|
16.6
|
1.0
|
|
OH
|
H:TYR228
|
4.5
|
12.7
|
1.0
|
|
C15
|
C:OGZ3
|
4.5
|
17.5
|
0.6
|
|
HA3
|
H:GLY216
|
4.5
|
16.9
|
1.0
|
|
O
|
H:HOH455
|
4.6
|
14.5
|
1.0
|
|
CA
|
H:CYS191
|
4.7
|
20.7
|
1.0
|
|
O
|
H:TRP215
|
4.7
|
12.4
|
1.0
|
|
C15
|
C:OGZ3
|
4.7
|
35.4
|
0.4
|
|
C
|
H:ASP189
|
4.7
|
14.6
|
1.0
|
|
H
|
H:PHE227
|
4.8
|
12.9
|
1.0
|
|
C16
|
C:OGZ3
|
4.9
|
18.8
|
0.6
|
|
Fluorine binding site 6 out
of 6 in 6y9h
Go back to
Fluorine Binding Sites List in 6y9h
Fluorine binding site 6 out
of 6 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F3
b:36.9
occ:0.44
|
F2
|
C:OGZ3
|
0.0
|
36.9
|
0.4
|
|
C20
|
C:OGZ3
|
1.3
|
36.7
|
0.4
|
|
OE2
|
H:GLU192
|
2.1
|
29.3
|
0.6
|
|
F
|
C:OGZ3
|
2.1
|
37.0
|
0.4
|
|
F1
|
C:OGZ3
|
2.1
|
36.9
|
0.4
|
|
C19
|
C:OGZ3
|
2.4
|
36.0
|
0.4
|
|
O
|
C:HOH103
|
2.8
|
28.4
|
1.0
|
|
C21
|
C:OGZ3
|
2.8
|
35.6
|
0.4
|
|
C17
|
C:OGZ3
|
3.0
|
19.6
|
0.6
|
|
C16
|
C:OGZ3
|
3.1
|
18.8
|
0.6
|
|
CD
|
H:GLU192
|
3.1
|
28.6
|
0.6
|
|
N
|
C:DPN1
|
3.2
|
15.1
|
0.6
|
|
N
|
C:DPN1
|
3.3
|
37.0
|
0.4
|
|
H
|
H:GLY219
|
3.4
|
23.6
|
1.0
|
|
O
|
H:GLY216
|
3.5
|
18.6
|
1.0
|
|
C18
|
C:OGZ3
|
3.6
|
36.0
|
0.4
|
|
OE1
|
H:GLU192
|
3.7
|
30.0
|
0.6
|
|
O
|
C:DPN1
|
3.9
|
12.9
|
0.6
|
|
O
|
C:DPN1
|
3.9
|
36.9
|
0.4
|
|
O
|
C:PRO2
|
4.0
|
15.1
|
0.6
|
|
O
|
C:PRO2
|
4.1
|
36.5
|
0.4
|
|
N
|
H:GLY219
|
4.2
|
19.6
|
1.0
|
|
C15
|
C:OGZ3
|
4.2
|
35.4
|
0.4
|
|
HG3
|
H:GLU192
|
4.2
|
33.0
|
0.6
|
|
C
|
C:DPN1
|
4.3
|
12.9
|
0.6
|
|
C18
|
C:OGZ3
|
4.3
|
19.4
|
0.6
|
|
C
|
C:DPN1
|
4.3
|
36.8
|
0.4
|
|
CG
|
H:GLU192
|
4.3
|
27.5
|
0.6
|
|
H
|
H:GLY216
|
4.3
|
15.8
|
1.0
|
|
C15
|
C:OGZ3
|
4.3
|
17.5
|
0.6
|
|
C
|
H:GLY216
|
4.3
|
15.5
|
1.0
|
|
HA
|
H:GLU217
|
4.3
|
19.7
|
1.0
|
|
CA
|
C:DPN1
|
4.4
|
13.9
|
0.6
|
|
O
|
H:GLY219
|
4.4
|
22.5
|
1.0
|
|
CA
|
C:DPN1
|
4.4
|
36.8
|
0.4
|
|
HA2
|
H:GLY219
|
4.5
|
24.6
|
1.0
|
|
HG2
|
H:GLU192
|
4.6
|
33.0
|
0.6
|
|
C17
|
C:OGZ3
|
4.7
|
35.6
|
0.4
|
|
C
|
C:PRO2
|
4.7
|
13.7
|
0.6
|
|
CA
|
H:GLY219
|
4.7
|
20.4
|
1.0
|
|
C
|
C:PRO2
|
4.8
|
36.1
|
0.4
|
|
C
|
H:GLY219
|
4.9
|
21.1
|
1.0
|
|
C16
|
C:OGZ3
|
4.9
|
35.3
|
0.4
|
|
HB2
|
H:GLU192
|
4.9
|
25.9
|
0.4
|
|
CA
|
H:GLU217
|
5.0
|
16.4
|
1.0
|
|
N
|
H:GLU217
|
5.0
|
14.9
|
1.0
|
|
N
|
H:GLY216
|
5.0
|
13.1
|
1.0
|
|
Reference:
A.Sandner,
A.Heine,
G.Klebe.
Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) To Be Published.
Page generated: Fri Aug 2 04:27:52 2024
|
