Atomistry » Fluorine » PDB 5lck-5lz4 » 5lws
Atomistry »
  Fluorine »
    PDB 5lck-5lz4 »
      5lws »

Fluorine in PDB 5lws: Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof

Enzymatic activity of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof

All present enzymatic activity of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof:
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof, PDB code: 5lws 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) 36.55 / 1.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.327, 73.095, 53.029, 90.00, 109.83, 90.00
R / Rfree (%) 11.6 / 13.2

Other elements in 5lws:

The structure of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof (pdb code 5lws). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof, PDB code: 5lws:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5lws

Go back to Fluorine Binding Sites List in 5lws
Fluorine binding site 1 out of 6 in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:23.8
occ:0.57
F1 A:TFA411 0.0 23.8 0.6
C1 A:TFA411 0.3 35.6 0.4
O A:TFA411 1.3 35.6 0.4
C2 A:TFA411 1.4 20.9 0.6
OXT A:TFA411 1.4 36.0 0.4
C2 A:TFA411 1.4 34.1 0.4
F3 A:TFA411 2.2 30.4 0.4
F2 A:TFA411 2.2 35.6 0.4
F3 A:TFA411 2.2 18.4 0.6
F2 A:TFA411 2.3 21.1 0.6
C1 A:TFA411 2.4 22.3 0.6
F1 A:TFA411 2.4 34.6 0.4
HG A:SER289 3.1 9.9 0.3
O A:TFA411 3.1 26.0 0.6
OXT A:TFA411 3.1 18.2 0.6
HG23 A:VAL252 3.2 13.3 1.0
CE A:LYS243 3.4 22.2 1.0
HG21 A:VAL252 3.6 13.3 1.0
OG A:SER289 3.6 12.2 0.7
OG A:SER289 3.6 8.2 0.3
O A:HOH2468 3.7 31.5 1.0
HG2 A:LYS243 3.8 18.2 1.0
HB3 A:SER289 3.9 10.9 0.7
CG2 A:VAL252 3.9 11.1 1.0
HB2 A:SER289 3.9 9.2 0.3
O A:HOH2492 3.9 46.1 1.0
HD3 A:LYS243 4.1 23.4 1.0
CD A:LYS243 4.2 19.5 1.0
HG A:SER289 4.3 14.7 0.7
CB A:SER289 4.3 9.1 0.7
CB A:SER289 4.3 7.7 0.3
CG A:LYS243 4.5 15.2 1.0
O A:GLY241 4.5 12.0 1.0
HB A:VAL252 4.6 10.5 1.0
HG22 A:VAL252 4.6 13.3 1.0
HA A:SER289 4.7 9.2 0.3
HA A:SER289 4.7 9.6 0.7
HA A:PHE253 4.8 8.3 1.0
HG3 A:LYS243 4.8 18.2 1.0
CB A:VAL252 4.9 8.8 1.0
HD3 A:PRO254 4.9 11.2 1.0
HG3 A:PRO254 5.0 12.5 1.0

Fluorine binding site 2 out of 6 in 5lws

Go back to Fluorine Binding Sites List in 5lws
Fluorine binding site 2 out of 6 in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:34.6
occ:0.43
F1 A:TFA411 0.0 34.6 0.4
C1 A:TFA411 0.1 22.3 0.6
OXT A:TFA411 1.2 18.2 0.6
O A:TFA411 1.3 26.0 0.6
C2 A:TFA411 1.4 34.1 0.4
C2 A:TFA411 1.6 20.9 0.6
F3 A:TFA411 2.2 30.4 0.4
F2 A:TFA411 2.2 35.6 0.4
F3 A:TFA411 2.4 18.4 0.6
C1 A:TFA411 2.4 35.6 0.4
F2 A:TFA411 2.4 21.1 0.6
F1 A:TFA411 2.4 23.8 0.6
OXT A:TFA411 3.0 36.0 0.4
HA A:PRO254 3.1 10.3 1.0
HG3 A:PRO254 3.1 12.5 1.0
O A:TFA411 3.2 35.6 0.4
O A:HOH2483 3.5 12.8 1.0
HG A:SER289 3.6 9.9 0.3
OG A:SER289 3.6 12.2 0.7
CA A:PRO254 3.7 8.6 1.0
HA A:SER289 3.7 9.6 0.7
HA A:SER289 3.7 9.2 0.3
N A:PRO254 3.7 8.1 1.0
CG A:PRO254 3.8 10.4 1.0
O A:HOH2468 3.8 31.5 1.0
HB3 A:PRO254 3.9 12.7 1.0
HD3 A:PRO254 3.9 11.2 1.0
HB2 A:SER289 3.9 9.2 0.3
HG A:SER289 4.0 14.7 0.7
CB A:PRO254 4.0 10.5 1.0
CD A:PRO254 4.1 9.3 1.0
C A:PHE253 4.1 6.8 1.0
OG A:SER289 4.3 8.2 0.3
HB3 A:SER289 4.3 10.9 0.7
O A:PHE253 4.3 7.0 1.0
CB A:SER289 4.3 9.1 0.7
CB A:SER289 4.4 7.7 0.3
CA A:SER289 4.4 8.0 0.7
CA A:SER289 4.4 7.7 0.3
HA A:PHE253 4.5 8.3 1.0
O A:SER288 4.6 9.1 1.0
HG2 A:PRO254 4.6 12.5 1.0
O A:GLY241 4.6 12.0 1.0
CA A:PHE253 4.8 7.0 1.0
HG23 A:VAL252 4.9 13.3 1.0
O A:HOH2492 4.9 46.1 1.0

Fluorine binding site 3 out of 6 in 5lws

Go back to Fluorine Binding Sites List in 5lws
Fluorine binding site 3 out of 6 in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:21.1
occ:0.57
F2 A:TFA411 0.0 21.1 0.6
F2 A:TFA411 0.2 35.6 0.4
C2 A:TFA411 1.4 20.9 0.6
C2 A:TFA411 1.5 34.1 0.4
F3 A:TFA411 2.1 18.4 0.6
F3 A:TFA411 2.2 30.4 0.4
F1 A:TFA411 2.3 23.8 0.6
C1 A:TFA411 2.4 22.3 0.6
F1 A:TFA411 2.4 34.6 0.4
C1 A:TFA411 2.5 35.6 0.4
HA A:PHE253 2.7 8.3 1.0
HD3 A:PRO254 2.8 11.2 1.0
O A:TFA411 2.8 26.0 0.6
O A:GLY241 2.8 12.0 1.0
OXT A:TFA411 2.9 36.0 0.4
HG23 A:VAL252 3.2 13.3 1.0
O A:HOH2468 3.3 31.5 1.0
CA A:PHE253 3.4 7.0 1.0
OXT A:TFA411 3.4 18.2 0.6
HG3 A:PRO254 3.4 12.5 1.0
O A:TFA411 3.5 35.6 0.4
CD A:PRO254 3.5 9.3 1.0
C A:PHE253 3.5 6.8 1.0
HA A:ALA242 3.5 10.6 1.0
N A:PRO254 3.5 8.1 1.0
HG2 A:LYS243 3.6 18.2 1.0
HG A:SER289 3.7 9.9 0.3
N A:PHE253 3.8 7.0 1.0
C A:GLY241 3.8 10.1 1.0
O A:VAL252 3.8 8.4 1.0
C A:VAL252 4.0 7.3 1.0
CG A:PRO254 4.0 10.4 1.0
HA A:PRO254 4.1 10.3 1.0
CG2 A:VAL252 4.1 11.1 1.0
O A:PHE253 4.2 7.0 1.0
H A:PHE253 4.2 8.4 1.0
CA A:ALA242 4.3 8.9 1.0
HD2 A:PRO254 4.3 11.2 1.0
H A:LYS243 4.3 11.5 1.0
CA A:PRO254 4.3 8.6 1.0
HG21 A:VAL252 4.4 13.3 1.0
HA3 A:GLY241 4.5 13.5 1.0
N A:ALA242 4.5 9.1 1.0
OG A:SER289 4.5 8.2 0.3
HB A:VAL252 4.5 10.5 1.0
CG A:LYS243 4.5 15.2 1.0
HD3 A:LYS243 4.6 23.4 1.0
CE A:LYS243 4.6 22.2 1.0
N A:LYS243 4.7 9.6 1.0
HG2 A:PRO254 4.7 12.5 1.0
HG22 A:VAL252 4.7 13.3 1.0
CA A:GLY241 4.7 11.2 1.0
HB3 A:SER289 4.7 10.9 0.7
O A:HOH2492 4.8 46.1 1.0
C A:ALA242 4.8 9.5 1.0
CB A:PHE253 4.8 7.8 1.0
CB A:PRO254 4.8 10.5 1.0
HA A:SER289 4.8 9.6 0.7
CB A:VAL252 4.8 8.8 1.0
HA A:SER289 4.8 9.2 0.3
CD A:LYS243 4.8 19.5 1.0
HB2 A:PHE253 4.9 9.4 1.0
OG A:SER289 5.0 12.2 0.7

Fluorine binding site 4 out of 6 in 5lws

Go back to Fluorine Binding Sites List in 5lws
Fluorine binding site 4 out of 6 in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:35.6
occ:0.43
F2 A:TFA411 0.0 35.6 0.4
F2 A:TFA411 0.2 21.1 0.6
C2 A:TFA411 1.3 20.9 0.6
C2 A:TFA411 1.4 34.1 0.4
C1 A:TFA411 2.2 22.3 0.6
F1 A:TFA411 2.2 23.8 0.6
F3 A:TFA411 2.2 18.4 0.6
F3 A:TFA411 2.2 30.4 0.4
F1 A:TFA411 2.2 34.6 0.4
C1 A:TFA411 2.4 35.6 0.4
O A:TFA411 2.5 26.0 0.6
OXT A:TFA411 2.8 36.0 0.4
HD3 A:PRO254 2.8 11.2 1.0
O A:GLY241 2.8 12.0 1.0
HA A:PHE253 2.9 8.3 1.0
O A:HOH2468 3.1 31.5 1.0
OXT A:TFA411 3.3 18.2 0.6
HG3 A:PRO254 3.3 12.5 1.0
HG23 A:VAL252 3.4 13.3 1.0
O A:TFA411 3.4 35.6 0.4
CD A:PRO254 3.5 9.3 1.0
N A:PRO254 3.5 8.1 1.0
C A:PHE253 3.6 6.8 1.0
CA A:PHE253 3.6 7.0 1.0
HA A:ALA242 3.7 10.6 1.0
HG2 A:LYS243 3.7 18.2 1.0
HG A:SER289 3.8 9.9 0.3
C A:GLY241 3.8 10.1 1.0
CG A:PRO254 3.9 10.4 1.0
N A:PHE253 4.0 7.0 1.0
O A:VAL252 4.1 8.4 1.0
HA A:PRO254 4.1 10.3 1.0
C A:VAL252 4.2 7.3 1.0
O A:PHE253 4.3 7.0 1.0
CA A:PRO254 4.3 8.6 1.0
CG2 A:VAL252 4.3 11.1 1.0
HD2 A:PRO254 4.3 11.2 1.0
HA3 A:GLY241 4.3 13.5 1.0
H A:PHE253 4.4 8.4 1.0
CA A:ALA242 4.4 8.9 1.0
H A:LYS243 4.5 11.5 1.0
N A:ALA242 4.5 9.1 1.0
HG21 A:VAL252 4.5 13.3 1.0
HD3 A:LYS243 4.6 23.4 1.0
OG A:SER289 4.6 8.2 0.3
HG2 A:PRO254 4.6 12.5 1.0
O A:HOH2492 4.6 46.1 1.0
CG A:LYS243 4.6 15.2 1.0
CE A:LYS243 4.6 22.2 1.0
CA A:GLY241 4.7 11.2 1.0
CB A:PRO254 4.7 10.5 1.0
HB A:VAL252 4.7 10.5 1.0
HB3 A:SER289 4.8 10.9 0.7
HA A:SER289 4.8 9.6 0.7
HA A:SER289 4.8 9.2 0.3
N A:LYS243 4.8 9.6 1.0
CD A:LYS243 4.9 19.5 1.0
C A:ALA242 4.9 9.5 1.0
HG22 A:VAL252 4.9 13.3 1.0
OG A:SER289 4.9 12.2 0.7
HB3 A:PRO254 4.9 12.7 1.0
CB A:PHE253 4.9 7.8 1.0
HA2 A:GLY241 4.9 13.5 1.0

Fluorine binding site 5 out of 6 in 5lws

Go back to Fluorine Binding Sites List in 5lws
Fluorine binding site 5 out of 6 in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:18.4
occ:0.57
F3 A:TFA411 0.0 18.4 0.6
F3 A:TFA411 0.2 30.4 0.4
C2 A:TFA411 1.3 20.9 0.6
C2 A:TFA411 1.4 34.1 0.4
HG A:SER289 1.6 9.9 0.3
F2 A:TFA411 2.1 21.1 0.6
F2 A:TFA411 2.2 35.6 0.4
F1 A:TFA411 2.2 23.8 0.6
C1 A:TFA411 2.3 22.3 0.6
F1 A:TFA411 2.4 34.6 0.4
C1 A:TFA411 2.4 35.6 0.4
OG A:SER289 2.4 8.2 0.3
OXT A:TFA411 2.6 18.2 0.6
HB3 A:SER289 2.6 10.9 0.7
O A:TFA411 2.6 35.6 0.4
HA A:SER289 2.9 9.2 0.3
HA A:SER289 2.9 9.6 0.7
HG23 A:VAL252 3.0 13.3 1.0
OG A:SER289 3.2 12.2 0.7
CB A:SER289 3.2 9.1 0.7
HB2 A:SER289 3.2 9.2 0.3
CB A:SER289 3.2 7.7 0.3
HB A:VAL252 3.2 10.5 1.0
O A:PHE253 3.2 7.0 1.0
C A:PHE253 3.2 6.8 1.0
H A:PHE253 3.4 8.4 1.0
N A:PHE253 3.4 7.0 1.0
O A:TFA411 3.5 26.0 0.6
HA A:PHE253 3.5 8.3 1.0
CA A:SER289 3.5 8.0 0.7
CA A:SER289 3.5 7.7 0.3
OXT A:TFA411 3.5 36.0 0.4
CG2 A:VAL252 3.6 11.1 1.0
HG21 A:VAL252 3.6 13.3 1.0
CA A:PHE253 3.6 7.0 1.0
H A:CYS290 3.6 8.6 1.0
HA A:PRO254 3.7 10.3 1.0
N A:PRO254 3.7 8.1 1.0
CB A:VAL252 3.8 8.8 1.0
HG A:SER289 3.9 14.7 0.7
C A:VAL252 3.9 7.3 1.0
HB2 A:SER289 4.1 10.9 0.7
HB3 A:SER289 4.1 9.2 0.3
HD3 A:PRO254 4.1 11.2 1.0
N A:CYS290 4.2 7.1 1.0
CA A:PRO254 4.2 8.6 1.0
C A:SER289 4.3 7.3 0.3
C A:SER289 4.3 7.3 0.7
O A:VAL252 4.4 8.4 1.0
CD A:PRO254 4.5 9.3 1.0
HG22 A:VAL252 4.5 13.3 1.0
CA A:VAL252 4.5 7.6 1.0
HG3 A:PRO254 4.5 12.5 1.0
N A:SER289 4.7 7.2 0.7
N A:SER289 4.7 7.6 0.3
O A:CYS290 4.8 8.2 1.0
HG2 A:LYS243 4.8 18.2 1.0
O A:SER288 4.9 9.1 1.0
CG A:PRO254 4.9 10.4 1.0
HA A:VAL252 5.0 9.1 1.0
O A:GLY241 5.0 12.0 1.0

Fluorine binding site 6 out of 6 in 5lws

Go back to Fluorine Binding Sites List in 5lws
Fluorine binding site 6 out of 6 in the Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Endothiapepsin in Complex with Fragment 177 and A Derivative Thereof within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:30.4
occ:0.43
F3 A:TFA411 0.0 30.4 0.4
F3 A:TFA411 0.2 18.4 0.6
C2 A:TFA411 1.3 20.9 0.6
C2 A:TFA411 1.4 34.1 0.4
HG A:SER289 1.6 9.9 0.3
F2 A:TFA411 2.2 21.1 0.6
F1 A:TFA411 2.2 23.8 0.6
C1 A:TFA411 2.2 22.3 0.6
F2 A:TFA411 2.2 35.6 0.4
F1 A:TFA411 2.2 34.6 0.4
C1 A:TFA411 2.3 35.6 0.4
OXT A:TFA411 2.5 18.2 0.6
OG A:SER289 2.5 8.2 0.3
O A:TFA411 2.6 35.6 0.4
HB3 A:SER289 2.6 10.9 0.7
HA A:SER289 2.8 9.2 0.3
HA A:SER289 2.8 9.6 0.7
OG A:SER289 3.1 12.2 0.7
HB2 A:SER289 3.1 9.2 0.3
HG23 A:VAL252 3.1 13.3 1.0
CB A:SER289 3.1 9.1 0.7
CB A:SER289 3.2 7.7 0.3
O A:PHE253 3.2 7.0 1.0
C A:PHE253 3.3 6.8 1.0
O A:TFA411 3.4 26.0 0.6
HB A:VAL252 3.4 10.5 1.0
CA A:SER289 3.4 8.0 0.7
CA A:SER289 3.4 7.7 0.3
OXT A:TFA411 3.5 36.0 0.4
H A:PHE253 3.5 8.4 1.0
N A:PHE253 3.5 7.0 1.0
HA A:PRO254 3.6 10.3 1.0
HA A:PHE253 3.6 8.3 1.0
H A:CYS290 3.6 8.6 1.0
CA A:PHE253 3.7 7.0 1.0
N A:PRO254 3.7 8.1 1.0
HG21 A:VAL252 3.7 13.3 1.0
CG2 A:VAL252 3.7 11.1 1.0
HG A:SER289 3.8 14.7 0.7
CB A:VAL252 4.0 8.8 1.0
HB2 A:SER289 4.0 10.9 0.7
C A:VAL252 4.1 7.3 1.0
HB3 A:SER289 4.1 9.2 0.3
HD3 A:PRO254 4.1 11.2 1.0
CA A:PRO254 4.1 8.6 1.0
N A:CYS290 4.2 7.1 1.0
C A:SER289 4.3 7.3 0.3
C A:SER289 4.3 7.3 0.7
CD A:PRO254 4.4 9.3 1.0
HG3 A:PRO254 4.4 12.5 1.0
O A:VAL252 4.5 8.4 1.0
N A:SER289 4.6 7.2 0.7
N A:SER289 4.6 7.6 0.3
HG22 A:VAL252 4.6 13.3 1.0
CA A:VAL252 4.7 7.6 1.0
O A:SER288 4.8 9.1 1.0
O A:CYS290 4.9 8.2 1.0
HG2 A:LYS243 4.9 18.2 1.0
CG A:PRO254 4.9 10.4 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 11:31:14 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy