Fluorine in PDB 5lwu: Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
Enzymatic activity of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
All present enzymatic activity of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177:
3.4.23.22;
Protein crystallography data
The structure of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177, PDB code: 5lwu
was solved by
J.Schiebel,
A.Heine,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.77 /
1.11
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.325,
73.340,
53.063,
90.00,
109.86,
90.00
|
|
R / Rfree (%)
|
12.3 /
14.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
(pdb code 5lwu). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the
Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177, PDB code: 5lwu:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Fluorine binding site 1 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 1 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:15.8
occ:0.40
|
F1
|
A:TFA403
|
0.0
|
15.8
|
0.4
|
|
C1
|
A:TFA403
|
0.4
|
46.2
|
0.6
|
|
C2
|
A:TFA403
|
1.4
|
14.0
|
0.4
|
|
O
|
A:TFA403
|
1.4
|
46.1
|
0.6
|
|
OXT
|
A:TFA403
|
1.4
|
46.0
|
0.6
|
|
C2
|
A:TFA403
|
1.4
|
46.3
|
0.6
|
|
F1
|
A:TFA403
|
2.1
|
46.5
|
0.6
|
|
F2
|
A:TFA403
|
2.1
|
46.0
|
0.6
|
|
F2
|
A:TFA403
|
2.2
|
12.2
|
0.4
|
|
F3
|
A:TFA403
|
2.2
|
14.1
|
0.4
|
|
C1
|
A:TFA403
|
2.4
|
14.1
|
0.4
|
|
F3
|
A:TFA403
|
2.5
|
46.3
|
0.6
|
|
O
|
A:TFA403
|
3.1
|
15.2
|
0.4
|
|
OXT
|
A:TFA403
|
3.1
|
13.4
|
0.4
|
|
HG23
|
A:VAL252
|
3.2
|
13.8
|
1.0
|
|
CE
|
A:LYS243
|
3.4
|
20.8
|
1.0
|
|
HG
|
A:SER289
|
3.5
|
14.6
|
0.8
|
|
HG
|
A:SER289
|
3.5
|
10.6
|
0.2
|
|
HG21
|
A:VAL252
|
3.6
|
13.8
|
1.0
|
|
OG
|
A:SER289
|
3.6
|
8.8
|
0.2
|
|
OG
|
A:SER289
|
3.6
|
12.1
|
0.8
|
|
O
|
A:HOH546
|
3.7
|
30.3
|
1.0
|
|
HB2
|
A:SER289
|
3.8
|
10.2
|
0.2
|
|
CG2
|
A:VAL252
|
3.8
|
11.5
|
1.0
|
|
HB3
|
A:SER289
|
3.9
|
12.1
|
0.8
|
|
HG2
|
A:LYS243
|
3.9
|
18.9
|
1.0
|
|
O
|
A:HOH526
|
3.9
|
39.4
|
1.0
|
|
HD3
|
A:LYS243
|
4.2
|
23.0
|
1.0
|
|
CB
|
A:SER289
|
4.3
|
8.5
|
0.2
|
|
CB
|
A:SER289
|
4.3
|
10.1
|
0.8
|
|
CD
|
A:LYS243
|
4.3
|
19.2
|
1.0
|
|
HB
|
A:VAL252
|
4.4
|
12.0
|
1.0
|
|
HG22
|
A:VAL252
|
4.5
|
13.8
|
1.0
|
|
CG
|
A:LYS243
|
4.5
|
15.8
|
1.0
|
|
O
|
A:GLY241
|
4.6
|
12.5
|
1.0
|
|
HA
|
A:SER289
|
4.6
|
10.0
|
0.2
|
|
HA
|
A:SER289
|
4.6
|
10.3
|
0.8
|
|
CB
|
A:VAL252
|
4.8
|
10.0
|
1.0
|
|
HA
|
A:PHE253
|
4.8
|
9.7
|
1.0
|
|
HG3
|
A:LYS243
|
4.9
|
18.9
|
1.0
|
|
HD3
|
A:PRO254
|
5.0
|
12.4
|
1.0
|
|
Fluorine binding site 2 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 2 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:46.5
occ:0.60
|
F1
|
A:TFA403
|
0.0
|
46.5
|
0.6
|
|
F3
|
A:TFA403
|
0.4
|
14.1
|
0.4
|
|
C2
|
A:TFA403
|
1.2
|
14.0
|
0.4
|
|
C2
|
A:TFA403
|
1.4
|
46.3
|
0.6
|
|
C1
|
A:TFA403
|
2.1
|
14.1
|
0.4
|
|
F1
|
A:TFA403
|
2.1
|
15.8
|
0.4
|
|
F2
|
A:TFA403
|
2.2
|
46.0
|
0.6
|
|
F3
|
A:TFA403
|
2.2
|
46.3
|
0.6
|
|
F2
|
A:TFA403
|
2.3
|
12.2
|
0.4
|
|
C1
|
A:TFA403
|
2.4
|
46.2
|
0.6
|
|
O
|
A:TFA403
|
2.4
|
15.2
|
0.4
|
|
OXT
|
A:TFA403
|
2.7
|
46.0
|
0.6
|
|
HD3
|
A:PRO254
|
2.8
|
12.4
|
1.0
|
|
O
|
A:GLY241
|
2.9
|
12.5
|
1.0
|
|
O
|
A:HOH546
|
3.0
|
30.3
|
1.0
|
|
HA
|
A:PHE253
|
3.1
|
9.7
|
1.0
|
|
OXT
|
A:TFA403
|
3.2
|
13.4
|
0.4
|
|
HG3
|
A:PRO254
|
3.3
|
13.6
|
1.0
|
|
O
|
A:TFA403
|
3.5
|
46.1
|
0.6
|
|
HG23
|
A:VAL252
|
3.5
|
13.8
|
1.0
|
|
CD
|
A:PRO254
|
3.5
|
10.3
|
1.0
|
|
N
|
A:PRO254
|
3.5
|
9.1
|
1.0
|
|
C
|
A:PHE253
|
3.6
|
8.1
|
1.0
|
|
CA
|
A:PHE253
|
3.7
|
8.1
|
1.0
|
|
HA
|
A:ALA242
|
3.8
|
11.6
|
1.0
|
|
HG2
|
A:LYS243
|
3.8
|
18.9
|
1.0
|
|
CG
|
A:PRO254
|
3.9
|
11.3
|
1.0
|
|
C
|
A:GLY241
|
3.9
|
11.0
|
1.0
|
|
HA
|
A:PRO254
|
4.0
|
11.6
|
1.0
|
|
N
|
A:PHE253
|
4.1
|
8.1
|
1.0
|
|
O
|
A:VAL252
|
4.2
|
9.2
|
1.0
|
|
CA
|
A:PRO254
|
4.3
|
9.7
|
1.0
|
|
O
|
A:PHE253
|
4.3
|
8.2
|
1.0
|
|
C
|
A:VAL252
|
4.3
|
8.3
|
1.0
|
|
HD2
|
A:PRO254
|
4.4
|
12.4
|
1.0
|
|
CG2
|
A:VAL252
|
4.4
|
11.5
|
1.0
|
|
HA3
|
A:GLY241
|
4.4
|
14.2
|
1.0
|
|
H
|
A:PHE253
|
4.5
|
9.7
|
1.0
|
|
HG21
|
A:VAL252
|
4.6
|
13.8
|
1.0
|
|
CA
|
A:ALA242
|
4.6
|
9.6
|
1.0
|
|
HD3
|
A:LYS243
|
4.6
|
23.0
|
1.0
|
|
OG
|
A:SER289
|
4.6
|
8.8
|
0.2
|
|
CE
|
A:LYS243
|
4.6
|
20.8
|
1.0
|
|
HG2
|
A:PRO254
|
4.6
|
13.6
|
1.0
|
|
N
|
A:ALA242
|
4.6
|
9.6
|
1.0
|
|
CB
|
A:PRO254
|
4.6
|
11.3
|
1.0
|
|
H
|
A:LYS243
|
4.7
|
12.9
|
1.0
|
|
HB
|
A:VAL252
|
4.7
|
12.0
|
1.0
|
|
CA
|
A:GLY241
|
4.7
|
11.8
|
1.0
|
|
CG
|
A:LYS243
|
4.7
|
15.8
|
1.0
|
|
HA
|
A:SER289
|
4.8
|
10.0
|
0.2
|
|
HA
|
A:SER289
|
4.8
|
10.3
|
0.8
|
|
HG
|
A:SER289
|
4.8
|
10.6
|
0.2
|
|
HB3
|
A:SER289
|
4.8
|
12.1
|
0.8
|
|
HB3
|
A:PRO254
|
4.8
|
13.5
|
1.0
|
|
OG
|
A:SER289
|
4.9
|
12.1
|
0.8
|
|
CD
|
A:LYS243
|
4.9
|
19.2
|
1.0
|
|
N
|
A:LYS243
|
5.0
|
10.7
|
1.0
|
|
HA2
|
A:GLY241
|
5.0
|
14.2
|
1.0
|
|
Fluorine binding site 3 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 3 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:12.2
occ:0.40
|
F2
|
A:TFA403
|
0.0
|
12.2
|
0.4
|
|
F2
|
A:TFA403
|
0.1
|
46.0
|
0.6
|
|
C2
|
A:TFA403
|
1.3
|
14.0
|
0.4
|
|
C2
|
A:TFA403
|
1.4
|
46.3
|
0.6
|
|
F3
|
A:TFA403
|
2.2
|
14.1
|
0.4
|
|
F1
|
A:TFA403
|
2.2
|
15.8
|
0.4
|
|
F3
|
A:TFA403
|
2.2
|
46.3
|
0.6
|
|
F1
|
A:TFA403
|
2.3
|
46.5
|
0.6
|
|
C1
|
A:TFA403
|
2.3
|
14.1
|
0.4
|
|
C1
|
A:TFA403
|
2.4
|
46.2
|
0.6
|
|
OG
|
A:SER289
|
2.4
|
8.8
|
0.2
|
|
OXT
|
A:TFA403
|
2.6
|
13.4
|
0.4
|
|
HB3
|
A:SER289
|
2.6
|
12.1
|
0.8
|
|
O
|
A:TFA403
|
2.7
|
46.1
|
0.6
|
|
HG
|
A:SER289
|
2.8
|
10.6
|
0.2
|
|
HA
|
A:SER289
|
2.9
|
10.0
|
0.2
|
|
HA
|
A:SER289
|
2.9
|
10.3
|
0.8
|
|
HG23
|
A:VAL252
|
3.0
|
13.8
|
1.0
|
|
HB
|
A:VAL252
|
3.1
|
12.0
|
1.0
|
|
HB2
|
A:SER289
|
3.1
|
10.2
|
0.2
|
|
CB
|
A:SER289
|
3.2
|
8.5
|
0.2
|
|
CB
|
A:SER289
|
3.2
|
10.1
|
0.8
|
|
OG
|
A:SER289
|
3.2
|
12.1
|
0.8
|
|
O
|
A:PHE253
|
3.2
|
8.2
|
1.0
|
|
C
|
A:PHE253
|
3.3
|
8.1
|
1.0
|
|
H
|
A:PHE253
|
3.4
|
9.7
|
1.0
|
|
N
|
A:PHE253
|
3.4
|
8.1
|
1.0
|
|
HG
|
A:SER289
|
3.4
|
14.6
|
0.8
|
|
CA
|
A:SER289
|
3.5
|
8.3
|
0.2
|
|
O
|
A:TFA403
|
3.5
|
15.2
|
0.4
|
|
CA
|
A:SER289
|
3.5
|
8.6
|
0.8
|
|
OXT
|
A:TFA403
|
3.5
|
46.0
|
0.6
|
|
HA
|
A:PHE253
|
3.5
|
9.7
|
1.0
|
|
HG21
|
A:VAL252
|
3.6
|
13.8
|
1.0
|
|
H
|
A:CYS290
|
3.6
|
9.8
|
1.0
|
|
CG2
|
A:VAL252
|
3.6
|
11.5
|
1.0
|
|
CA
|
A:PHE253
|
3.6
|
8.1
|
1.0
|
|
HA
|
A:PRO254
|
3.7
|
11.6
|
1.0
|
|
N
|
A:PRO254
|
3.8
|
9.1
|
1.0
|
|
CB
|
A:VAL252
|
3.8
|
10.0
|
1.0
|
|
C
|
A:VAL252
|
3.9
|
8.3
|
1.0
|
|
HB3
|
A:SER289
|
4.1
|
10.2
|
0.2
|
|
HB2
|
A:SER289
|
4.1
|
12.1
|
0.8
|
|
N
|
A:CYS290
|
4.1
|
8.2
|
1.0
|
|
HD3
|
A:PRO254
|
4.2
|
12.4
|
1.0
|
|
C
|
A:SER289
|
4.2
|
8.3
|
0.2
|
|
CA
|
A:PRO254
|
4.2
|
9.7
|
1.0
|
|
C
|
A:SER289
|
4.3
|
8.4
|
0.8
|
|
O
|
A:VAL252
|
4.4
|
9.2
|
1.0
|
|
CA
|
A:VAL252
|
4.5
|
8.7
|
1.0
|
|
O
|
A:HOH526
|
4.5
|
39.4
|
1.0
|
|
HG22
|
A:VAL252
|
4.5
|
13.8
|
1.0
|
|
CD
|
A:PRO254
|
4.5
|
10.3
|
1.0
|
|
HG3
|
A:PRO254
|
4.6
|
13.6
|
1.0
|
|
N
|
A:SER289
|
4.7
|
8.4
|
0.2
|
|
N
|
A:SER289
|
4.7
|
8.2
|
0.8
|
|
O
|
A:CYS290
|
4.7
|
8.8
|
1.0
|
|
HG2
|
A:LYS243
|
4.8
|
18.9
|
1.0
|
|
O
|
A:SER288
|
4.9
|
9.9
|
1.0
|
|
HA
|
A:VAL252
|
4.9
|
10.5
|
1.0
|
|
HG11
|
A:VAL252
|
5.0
|
13.4
|
1.0
|
|
Fluorine binding site 4 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 4 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:46.0
occ:0.60
|
F2
|
A:TFA403
|
0.0
|
46.0
|
0.6
|
|
F2
|
A:TFA403
|
0.1
|
12.2
|
0.4
|
|
C2
|
A:TFA403
|
1.3
|
14.0
|
0.4
|
|
C2
|
A:TFA403
|
1.4
|
46.3
|
0.6
|
|
F3
|
A:TFA403
|
2.1
|
14.1
|
0.4
|
|
F1
|
A:TFA403
|
2.1
|
15.8
|
0.4
|
|
F1
|
A:TFA403
|
2.2
|
46.5
|
0.6
|
|
F3
|
A:TFA403
|
2.2
|
46.3
|
0.6
|
|
C1
|
A:TFA403
|
2.3
|
14.1
|
0.4
|
|
C1
|
A:TFA403
|
2.4
|
46.2
|
0.6
|
|
OG
|
A:SER289
|
2.4
|
8.8
|
0.2
|
|
OXT
|
A:TFA403
|
2.6
|
13.4
|
0.4
|
|
HB3
|
A:SER289
|
2.7
|
12.1
|
0.8
|
|
O
|
A:TFA403
|
2.7
|
46.1
|
0.6
|
|
HG
|
A:SER289
|
2.8
|
10.6
|
0.2
|
|
HA
|
A:SER289
|
2.9
|
10.0
|
0.2
|
|
HA
|
A:SER289
|
2.9
|
10.3
|
0.8
|
|
HG23
|
A:VAL252
|
3.0
|
13.8
|
1.0
|
|
HB
|
A:VAL252
|
3.1
|
12.0
|
1.0
|
|
HB2
|
A:SER289
|
3.1
|
10.2
|
0.2
|
|
OG
|
A:SER289
|
3.2
|
12.1
|
0.8
|
|
CB
|
A:SER289
|
3.2
|
8.5
|
0.2
|
|
CB
|
A:SER289
|
3.2
|
10.1
|
0.8
|
|
O
|
A:PHE253
|
3.3
|
8.2
|
1.0
|
|
C
|
A:PHE253
|
3.3
|
8.1
|
1.0
|
|
H
|
A:PHE253
|
3.4
|
9.7
|
1.0
|
|
HG
|
A:SER289
|
3.4
|
14.6
|
0.8
|
|
N
|
A:PHE253
|
3.4
|
8.1
|
1.0
|
|
O
|
A:TFA403
|
3.4
|
15.2
|
0.4
|
|
OXT
|
A:TFA403
|
3.5
|
46.0
|
0.6
|
|
CA
|
A:SER289
|
3.5
|
8.3
|
0.2
|
|
CA
|
A:SER289
|
3.5
|
8.6
|
0.8
|
|
HG21
|
A:VAL252
|
3.6
|
13.8
|
1.0
|
|
HA
|
A:PHE253
|
3.6
|
9.7
|
1.0
|
|
CG2
|
A:VAL252
|
3.6
|
11.5
|
1.0
|
|
H
|
A:CYS290
|
3.6
|
9.8
|
1.0
|
|
CA
|
A:PHE253
|
3.7
|
8.1
|
1.0
|
|
HA
|
A:PRO254
|
3.7
|
11.6
|
1.0
|
|
N
|
A:PRO254
|
3.8
|
9.1
|
1.0
|
|
CB
|
A:VAL252
|
3.8
|
10.0
|
1.0
|
|
C
|
A:VAL252
|
3.9
|
8.3
|
1.0
|
|
HB3
|
A:SER289
|
4.1
|
10.2
|
0.2
|
|
HB2
|
A:SER289
|
4.1
|
12.1
|
0.8
|
|
N
|
A:CYS290
|
4.2
|
8.2
|
1.0
|
|
HD3
|
A:PRO254
|
4.2
|
12.4
|
1.0
|
|
CA
|
A:PRO254
|
4.3
|
9.7
|
1.0
|
|
C
|
A:SER289
|
4.3
|
8.3
|
0.2
|
|
C
|
A:SER289
|
4.3
|
8.4
|
0.8
|
|
O
|
A:VAL252
|
4.4
|
9.2
|
1.0
|
|
O
|
A:HOH526
|
4.5
|
39.4
|
1.0
|
|
HG22
|
A:VAL252
|
4.5
|
13.8
|
1.0
|
|
CA
|
A:VAL252
|
4.5
|
8.7
|
1.0
|
|
CD
|
A:PRO254
|
4.5
|
10.3
|
1.0
|
|
HG3
|
A:PRO254
|
4.6
|
13.6
|
1.0
|
|
N
|
A:SER289
|
4.7
|
8.4
|
0.2
|
|
N
|
A:SER289
|
4.7
|
8.2
|
0.8
|
|
O
|
A:CYS290
|
4.8
|
8.8
|
1.0
|
|
HG2
|
A:LYS243
|
4.8
|
18.9
|
1.0
|
|
O
|
A:SER288
|
4.9
|
9.9
|
1.0
|
|
HA
|
A:VAL252
|
4.9
|
10.5
|
1.0
|
|
Fluorine binding site 5 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 5 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:14.1
occ:0.40
|
F3
|
A:TFA403
|
0.0
|
14.1
|
0.4
|
|
F1
|
A:TFA403
|
0.4
|
46.5
|
0.6
|
|
C2
|
A:TFA403
|
1.4
|
14.0
|
0.4
|
|
C2
|
A:TFA403
|
1.5
|
46.3
|
0.6
|
|
F2
|
A:TFA403
|
2.1
|
46.0
|
0.6
|
|
F2
|
A:TFA403
|
2.2
|
12.2
|
0.4
|
|
F1
|
A:TFA403
|
2.2
|
15.8
|
0.4
|
|
C1
|
A:TFA403
|
2.4
|
14.1
|
0.4
|
|
F3
|
A:TFA403
|
2.5
|
46.3
|
0.6
|
|
C1
|
A:TFA403
|
2.5
|
46.2
|
0.6
|
|
HA
|
A:PHE253
|
2.8
|
9.7
|
1.0
|
|
HD3
|
A:PRO254
|
2.8
|
12.4
|
1.0
|
|
O
|
A:TFA403
|
2.8
|
15.2
|
0.4
|
|
O
|
A:GLY241
|
2.9
|
12.5
|
1.0
|
|
OXT
|
A:TFA403
|
2.9
|
46.0
|
0.6
|
|
HG23
|
A:VAL252
|
3.2
|
13.8
|
1.0
|
|
O
|
A:HOH546
|
3.3
|
30.3
|
1.0
|
|
CA
|
A:PHE253
|
3.4
|
8.1
|
1.0
|
|
OXT
|
A:TFA403
|
3.4
|
13.4
|
0.4
|
|
C
|
A:PHE253
|
3.5
|
8.1
|
1.0
|
|
CD
|
A:PRO254
|
3.5
|
10.3
|
1.0
|
|
N
|
A:PRO254
|
3.5
|
9.1
|
1.0
|
|
HG3
|
A:PRO254
|
3.5
|
13.6
|
1.0
|
|
O
|
A:TFA403
|
3.5
|
46.1
|
0.6
|
|
HA
|
A:ALA242
|
3.5
|
11.6
|
1.0
|
|
HG2
|
A:LYS243
|
3.6
|
18.9
|
1.0
|
|
N
|
A:PHE253
|
3.7
|
8.1
|
1.0
|
|
O
|
A:VAL252
|
3.8
|
9.2
|
1.0
|
|
C
|
A:GLY241
|
3.9
|
11.0
|
1.0
|
|
C
|
A:VAL252
|
3.9
|
8.3
|
1.0
|
|
CG
|
A:PRO254
|
4.0
|
11.3
|
1.0
|
|
CG2
|
A:VAL252
|
4.1
|
11.5
|
1.0
|
|
HA
|
A:PRO254
|
4.1
|
11.6
|
1.0
|
|
O
|
A:PHE253
|
4.1
|
8.2
|
1.0
|
|
H
|
A:PHE253
|
4.2
|
9.7
|
1.0
|
|
HD2
|
A:PRO254
|
4.3
|
12.4
|
1.0
|
|
CA
|
A:PRO254
|
4.3
|
9.7
|
1.0
|
|
HG21
|
A:VAL252
|
4.3
|
13.8
|
1.0
|
|
CA
|
A:ALA242
|
4.4
|
9.6
|
1.0
|
|
H
|
A:LYS243
|
4.4
|
12.9
|
1.0
|
|
HB
|
A:VAL252
|
4.4
|
12.0
|
1.0
|
|
OG
|
A:SER289
|
4.5
|
8.8
|
0.2
|
|
N
|
A:ALA242
|
4.5
|
9.6
|
1.0
|
|
HA3
|
A:GLY241
|
4.5
|
14.2
|
1.0
|
|
CG
|
A:LYS243
|
4.6
|
15.8
|
1.0
|
|
CE
|
A:LYS243
|
4.6
|
20.8
|
1.0
|
|
HD3
|
A:LYS243
|
4.6
|
23.0
|
1.0
|
|
HG
|
A:SER289
|
4.7
|
10.6
|
0.2
|
|
HG22
|
A:VAL252
|
4.7
|
13.8
|
1.0
|
|
N
|
A:LYS243
|
4.7
|
10.7
|
1.0
|
|
CB
|
A:VAL252
|
4.7
|
10.0
|
1.0
|
|
HG2
|
A:PRO254
|
4.8
|
13.6
|
1.0
|
|
HA
|
A:SER289
|
4.8
|
10.0
|
0.2
|
|
HB3
|
A:SER289
|
4.8
|
12.1
|
0.8
|
|
HA
|
A:SER289
|
4.8
|
10.3
|
0.8
|
|
CB
|
A:PRO254
|
4.8
|
11.3
|
1.0
|
|
CB
|
A:PHE253
|
4.8
|
8.5
|
1.0
|
|
CA
|
A:GLY241
|
4.8
|
11.8
|
1.0
|
|
C
|
A:ALA242
|
4.8
|
10.7
|
1.0
|
|
CD
|
A:LYS243
|
4.9
|
19.2
|
1.0
|
|
HB2
|
A:PHE253
|
4.9
|
10.2
|
1.0
|
|
OG
|
A:SER289
|
5.0
|
12.1
|
0.8
|
|
CA
|
A:VAL252
|
5.0
|
8.7
|
1.0
|
|
Fluorine binding site 6 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 6 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F403
b:46.3
occ:0.60
|
F3
|
A:TFA403
|
0.0
|
46.3
|
0.6
|
|
C1
|
A:TFA403
|
0.2
|
14.1
|
0.4
|
|
OXT
|
A:TFA403
|
1.0
|
13.4
|
0.4
|
|
C2
|
A:TFA403
|
1.4
|
46.3
|
0.6
|
|
O
|
A:TFA403
|
1.4
|
15.2
|
0.4
|
|
C2
|
A:TFA403
|
1.6
|
14.0
|
0.4
|
|
F2
|
A:TFA403
|
2.2
|
46.0
|
0.6
|
|
F1
|
A:TFA403
|
2.2
|
46.5
|
0.6
|
|
F2
|
A:TFA403
|
2.2
|
12.2
|
0.4
|
|
C1
|
A:TFA403
|
2.4
|
46.2
|
0.6
|
|
F1
|
A:TFA403
|
2.5
|
15.8
|
0.4
|
|
F3
|
A:TFA403
|
2.5
|
14.1
|
0.4
|
|
HA
|
A:PRO254
|
3.0
|
11.6
|
1.0
|
|
OXT
|
A:TFA403
|
3.1
|
46.0
|
0.6
|
|
O
|
A:TFA403
|
3.2
|
46.1
|
0.6
|
|
HG3
|
A:PRO254
|
3.3
|
13.6
|
1.0
|
|
OG
|
A:SER289
|
3.4
|
12.1
|
0.8
|
|
HA
|
A:SER289
|
3.4
|
10.0
|
0.2
|
|
HA
|
A:SER289
|
3.4
|
10.3
|
0.8
|
|
O
|
A:HOH674
|
3.5
|
14.6
|
1.0
|
|
HB2
|
A:SER289
|
3.6
|
10.2
|
0.2
|
|
CA
|
A:PRO254
|
3.7
|
9.7
|
1.0
|
|
N
|
A:PRO254
|
3.7
|
9.1
|
1.0
|
|
HG
|
A:SER289
|
3.8
|
14.6
|
0.8
|
|
HB3
|
A:PRO254
|
3.9
|
13.5
|
1.0
|
|
CG
|
A:PRO254
|
4.0
|
11.3
|
1.0
|
|
O
|
A:HOH546
|
4.0
|
30.3
|
1.0
|
|
HD3
|
A:PRO254
|
4.0
|
12.4
|
1.0
|
|
C
|
A:PHE253
|
4.0
|
8.1
|
1.0
|
|
OG
|
A:SER289
|
4.1
|
8.8
|
0.2
|
|
HB3
|
A:SER289
|
4.1
|
12.1
|
0.8
|
|
CB
|
A:SER289
|
4.1
|
8.5
|
0.2
|
|
CB
|
A:PRO254
|
4.1
|
11.3
|
1.0
|
|
CB
|
A:SER289
|
4.1
|
10.1
|
0.8
|
|
CA
|
A:SER289
|
4.2
|
8.3
|
0.2
|
|
CA
|
A:SER289
|
4.2
|
8.6
|
0.8
|
|
CD
|
A:PRO254
|
4.2
|
10.3
|
1.0
|
|
O
|
A:PHE253
|
4.2
|
8.2
|
1.0
|
|
HG
|
A:SER289
|
4.4
|
10.6
|
0.2
|
|
O
|
A:SER288
|
4.4
|
9.9
|
1.0
|
|
HA
|
A:PHE253
|
4.5
|
9.7
|
1.0
|
|
N
|
A:SER289
|
4.8
|
8.2
|
0.8
|
|
N
|
A:SER289
|
4.8
|
8.4
|
0.2
|
|
CA
|
A:PHE253
|
4.8
|
8.1
|
1.0
|
|
HG2
|
A:PRO254
|
4.9
|
13.6
|
1.0
|
|
HG23
|
A:VAL252
|
4.9
|
13.8
|
1.0
|
|
H
|
A:CYS255
|
4.9
|
10.6
|
1.0
|
|
O
|
A:GLY241
|
4.9
|
12.5
|
1.0
|
|
H
|
A:CYS290
|
4.9
|
9.8
|
1.0
|
|
C
|
A:SER288
|
4.9
|
8.6
|
1.0
|
|
Fluorine binding site 7 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 7 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F404
b:25.6
occ:0.62
|
F1
|
A:TFA404
|
0.0
|
25.6
|
0.6
|
|
C2
|
A:TFA404
|
1.4
|
25.6
|
0.6
|
|
F2
|
A:TFA404
|
2.2
|
25.6
|
0.6
|
|
F3
|
A:TFA404
|
2.2
|
27.4
|
0.6
|
|
C1
|
A:TFA404
|
2.3
|
23.9
|
0.6
|
|
HA
|
A:ASP146
|
2.6
|
15.1
|
1.0
|
|
O
|
A:TFA404
|
2.8
|
23.0
|
0.6
|
|
HB2
|
A:ASP146
|
3.0
|
17.4
|
1.0
|
|
HD1
|
A:PHE145
|
3.2
|
15.2
|
1.0
|
|
CA
|
A:ASP146
|
3.2
|
12.6
|
1.0
|
|
OXT
|
A:TFA404
|
3.3
|
23.4
|
0.6
|
|
CB
|
A:ASP146
|
3.4
|
14.5
|
1.0
|
|
O
|
A:HOH537
|
3.5
|
18.7
|
1.0
|
|
CG
|
A:ASP146
|
3.5
|
18.0
|
1.0
|
|
CD1
|
A:PHE145
|
3.5
|
12.7
|
1.0
|
|
CD
|
A:LYS149
|
3.5
|
17.4
|
0.5
|
|
N
|
A:ASP146
|
3.6
|
11.1
|
1.0
|
|
OD1
|
A:ASP146
|
3.6
|
20.9
|
1.0
|
|
O
|
A:HOH654
|
3.7
|
15.7
|
0.4
|
|
H
|
A:ASP146
|
3.7
|
13.3
|
1.0
|
|
HE1
|
A:PHE145
|
3.7
|
16.6
|
1.0
|
|
CE1
|
A:PHE145
|
3.9
|
13.8
|
1.0
|
|
CD
|
A:LYS149
|
4.2
|
19.2
|
0.5
|
|
C
|
A:PHE145
|
4.2
|
10.5
|
1.0
|
|
OD2
|
A:ASP146
|
4.2
|
18.8
|
1.0
|
|
HB2
|
A:LYS149
|
4.3
|
20.6
|
0.5
|
|
HG1
|
A:THR143
|
4.3
|
13.9
|
1.0
|
|
HB3
|
A:PHE145
|
4.3
|
12.6
|
1.0
|
|
HG2
|
A:LYS149
|
4.3
|
20.2
|
0.5
|
|
HB3
|
A:ASP146
|
4.3
|
17.4
|
1.0
|
|
CG
|
A:PHE145
|
4.4
|
10.8
|
1.0
|
|
O
|
A:PHE145
|
4.5
|
11.2
|
1.0
|
|
CG
|
A:LYS149
|
4.5
|
16.8
|
0.5
|
|
HB3
|
A:LYS149
|
4.6
|
19.2
|
0.5
|
|
OG1
|
A:THR143
|
4.6
|
11.6
|
1.0
|
|
C
|
A:ASP146
|
4.6
|
12.5
|
1.0
|
|
HD2
|
A:PHE130
|
4.6
|
16.2
|
1.0
|
|
CB
|
A:PHE145
|
4.8
|
10.5
|
1.0
|
|
CZ
|
A:PHE145
|
4.9
|
13.3
|
1.0
|
|
HA
|
A:PHE130
|
5.0
|
13.1
|
1.0
|
|
O
|
A:ASP146
|
5.0
|
14.0
|
1.0
|
|
Fluorine binding site 8 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 8 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F404
b:25.6
occ:0.62
|
F2
|
A:TFA404
|
0.0
|
25.6
|
0.6
|
|
C2
|
A:TFA404
|
1.4
|
25.6
|
0.6
|
|
F1
|
A:TFA404
|
2.2
|
25.6
|
0.6
|
|
F3
|
A:TFA404
|
2.2
|
27.4
|
0.6
|
|
C1
|
A:TFA404
|
2.4
|
23.9
|
0.6
|
|
O
|
A:TFA404
|
2.9
|
23.0
|
0.6
|
|
HD1
|
A:PHE145
|
2.9
|
15.2
|
1.0
|
|
O
|
A:HOH537
|
3.1
|
18.7
|
1.0
|
|
HE1
|
A:PHE145
|
3.2
|
16.6
|
1.0
|
|
HD2
|
A:PHE130
|
3.2
|
16.2
|
1.0
|
|
HE2
|
A:PHE130
|
3.3
|
15.8
|
1.0
|
|
OXT
|
A:TFA404
|
3.4
|
23.4
|
0.6
|
|
CD2
|
A:PHE130
|
3.5
|
13.5
|
1.0
|
|
CE2
|
A:PHE130
|
3.5
|
13.2
|
1.0
|
|
O
|
A:HOH654
|
3.5
|
15.7
|
0.4
|
|
HZ2
|
A:TRP195
|
3.6
|
12.5
|
1.0
|
|
CD1
|
A:PHE145
|
3.6
|
12.7
|
1.0
|
|
CE1
|
A:PHE145
|
3.7
|
13.8
|
1.0
|
|
HA
|
A:PHE130
|
3.7
|
13.1
|
1.0
|
|
CZ2
|
A:TRP195
|
4.2
|
10.4
|
1.0
|
|
CG
|
A:PHE130
|
4.4
|
11.9
|
1.0
|
|
CZ
|
A:PHE130
|
4.4
|
12.8
|
1.0
|
|
HB2
|
A:ASP146
|
4.5
|
17.4
|
1.0
|
|
HA3
|
A:GLY319
|
4.5
|
17.1
|
1.0
|
|
HH2
|
A:TRP195
|
4.6
|
12.4
|
1.0
|
|
O
|
A:ALA129
|
4.6
|
10.6
|
1.0
|
|
CA
|
A:PHE130
|
4.7
|
10.9
|
1.0
|
|
HG1
|
A:THR143
|
4.7
|
13.9
|
1.0
|
|
HA
|
A:ASP146
|
4.7
|
15.1
|
1.0
|
|
HB3
|
A:PHE145
|
4.7
|
12.6
|
1.0
|
|
CH2
|
A:TRP195
|
4.8
|
10.3
|
1.0
|
|
HZ
|
A:PHE130
|
4.8
|
15.3
|
1.0
|
|
HA2
|
A:GLY319
|
4.8
|
17.1
|
1.0
|
|
H
|
A:SER131
|
4.8
|
13.5
|
1.0
|
|
CG
|
A:PHE145
|
4.8
|
10.8
|
1.0
|
|
CZ
|
A:PHE145
|
5.0
|
13.3
|
1.0
|
|
Fluorine binding site 9 out
of 9 in 5lwu
Go back to
Fluorine Binding Sites List in 5lwu
Fluorine binding site 9 out
of 9 in the Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Structure Resulting From An Endothiapepsin Crystal Soaked with A Dimeric Derivative of Fragment 177 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F404
b:27.4
occ:0.62
|
F3
|
A:TFA404
|
0.0
|
27.4
|
0.6
|
|
C2
|
A:TFA404
|
1.4
|
25.6
|
0.6
|
|
F2
|
A:TFA404
|
2.2
|
25.6
|
0.6
|
|
F1
|
A:TFA404
|
2.2
|
25.6
|
0.6
|
|
C1
|
A:TFA404
|
2.4
|
23.9
|
0.6
|
|
OXT
|
A:TFA404
|
2.7
|
23.4
|
0.6
|
|
HE2
|
A:PHE130
|
3.3
|
15.8
|
1.0
|
|
HD2
|
A:PHE130
|
3.5
|
16.2
|
1.0
|
|
O
|
A:TFA404
|
3.5
|
23.0
|
0.6
|
|
O
|
A:HOH654
|
3.6
|
15.7
|
0.4
|
|
CD
|
A:LYS149
|
3.9
|
17.4
|
0.5
|
|
CE2
|
A:PHE130
|
4.0
|
13.2
|
1.0
|
|
HE1
|
A:PHE145
|
4.0
|
16.6
|
1.0
|
|
CD2
|
A:PHE130
|
4.0
|
13.5
|
1.0
|
|
HA3
|
A:GLY319
|
4.2
|
17.1
|
1.0
|
|
CD
|
A:LYS149
|
4.2
|
19.2
|
0.5
|
|
HA2
|
A:GLY319
|
4.4
|
17.1
|
1.0
|
|
O
|
A:GLY319
|
4.4
|
17.9
|
1.0
|
|
HD1
|
A:PHE145
|
4.5
|
15.2
|
1.0
|
|
HA
|
A:ASP146
|
4.5
|
15.1
|
1.0
|
|
CE1
|
A:PHE145
|
4.6
|
13.8
|
1.0
|
|
HG3
|
A:PRO323
|
4.6
|
18.6
|
1.0
|
|
CA
|
A:GLY319
|
4.7
|
14.2
|
1.0
|
|
OD1
|
A:ASP146
|
4.7
|
20.9
|
1.0
|
|
CD1
|
A:PHE145
|
4.8
|
12.7
|
1.0
|
|
O
|
A:HOH796
|
4.9
|
45.4
|
1.0
|
|
CG
|
A:ASP146
|
4.9
|
18.0
|
1.0
|
|
HB2
|
A:ASP146
|
4.9
|
17.4
|
1.0
|
|
O
|
A:HOH537
|
5.0
|
18.7
|
1.0
|
|
C
|
A:GLY319
|
5.0
|
16.2
|
1.0
|
|
Reference:
J.Cramer,
J.Schiebel,
T.Wulsdorf,
K.Grohe,
E.E.Najbauer,
F.R.Ehrmann,
N.Radeva,
N.Zitzer,
U.Linne,
R.Linser,
A.Heine,
G.Klebe.
A False-Positive Screening Hit in Fragment-Based Lead Discovery: Watch Out For the Red Herring. Angew. Chem. Int. Ed. Engl. V. 56 1908 2017.
ISSN: ESSN 1521-3773
PubMed: 28097765
DOI: 10.1002/ANIE.201609824
Page generated: Thu Aug 1 11:31:17 2024
|
