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Fluorine in PDB 5lwt: Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177

Enzymatic activity of Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177

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

Protein crystallography data

The structure of Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177, PDB code: 5lwt 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) 29.44 / 1.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.384, 73.125, 52.694, 90.00, 109.64, 90.00
R / Rfree (%) 12.8 / 14.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 (pdb code 5lwt). 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 A Methoxylated Derivative of Fragment 177, PDB code: 5lwt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5lwt

Go back to Fluorine Binding Sites List in 5lwt
Fluorine binding site 1 out of 6 in the Endothiapepsin in Complex with A Methoxylated 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 Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:16.9
occ:0.42
F1 A:TFA411 0.0 16.9 0.4
F1 A:TFA411 0.2 44.3 0.6
C2 A:TFA411 1.4 16.1 0.4
C2 A:TFA411 1.6 44.2 0.6
F2 A:TFA411 2.2 15.0 0.4
F3 A:TFA411 2.2 18.4 0.4
F3 A:TFA411 2.3 44.3 0.6
C1 A:TFA411 2.4 16.1 0.4
F2 A:TFA411 2.5 43.8 0.6
C1 A:TFA411 2.5 44.6 0.6
O A:TFA411 2.8 18.1 0.4
O A:GLY241 2.8 12.0 1.0
HA A:PHE253 2.8 8.1 1.0
HD3 A:PRO254 2.9 9.9 1.0
O A:TFA411 3.0 44.3 0.6
HG23 A:VAL252 3.1 12.3 1.0
O A:HOH2468 3.2 18.3 0.5
OXT A:TFA411 3.4 14.4 0.4
HG3 A:PRO254 3.5 12.3 1.0
CA A:PHE253 3.5 6.8 1.0
HA A:ALA242 3.5 10.2 1.0
OXT A:TFA411 3.5 44.8 0.6
C A:PHE253 3.6 6.6 1.0
CD A:PRO254 3.6 8.2 1.0
N A:PRO254 3.6 7.3 1.0
HG2 A:LYS243 3.6 18.0 1.0
O A:HOH2468 3.6 29.0 0.5
HE2 A:LYS243 3.8 27.1 1.0
N A:PHE253 3.8 6.8 1.0
C A:GLY241 3.8 9.9 1.0
O A:VAL252 3.8 8.0 1.0
HG A:SER289 3.9 11.3 0.2
C A:VAL252 4.0 7.3 1.0
CG A:PRO254 4.0 10.3 1.0
CG2 A:VAL252 4.1 10.2 1.0
HA A:PRO254 4.2 9.4 1.0
O A:PHE253 4.2 7.0 1.0
H A:PHE253 4.2 8.1 1.0
HG A:SER289 4.3 13.8 0.8
HD3 A:LYS243 4.3 23.1 1.0
H A:LYS243 4.3 11.2 1.0
HG21 A:VAL252 4.3 12.3 1.0
CA A:ALA242 4.3 8.5 1.0
HD2 A:PRO254 4.4 9.9 1.0
CA A:PRO254 4.4 7.8 1.0
HB A:VAL252 4.5 10.8 1.0
N A:ALA242 4.5 8.4 1.0
HA3 A:GLY241 4.5 12.9 1.0
CG A:LYS243 4.5 15.0 1.0
CE A:LYS243 4.6 22.6 1.0
N A:LYS243 4.6 9.3 1.0
HG22 A:VAL252 4.7 12.3 1.0
CD A:LYS243 4.7 19.2 1.0
OG A:SER289 4.7 9.4 0.2
HZ3 A:LYS243 4.7 30.4 1.0
CB A:VAL252 4.7 9.0 1.0
CA A:GLY241 4.8 10.8 1.0
HB3 A:SER289 4.8 11.5 0.8
HG2 A:PRO254 4.8 12.3 1.0
HA A:SER289 4.8 9.3 0.2
C A:ALA242 4.8 9.5 1.0
HA A:SER289 4.8 9.4 0.8
CB A:PRO254 4.9 9.7 1.0
CB A:PHE253 4.9 7.4 1.0
OG A:SER289 5.0 11.5 0.8
CA A:VAL252 5.0 7.7 1.0
HB2 A:PHE253 5.0 8.9 1.0

Fluorine binding site 2 out of 6 in 5lwt

Go back to Fluorine Binding Sites List in 5lwt
Fluorine binding site 2 out of 6 in the Endothiapepsin in Complex with A Methoxylated 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 Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:44.3
occ:0.58
F1 A:TFA411 0.0 44.3 0.6
F1 A:TFA411 0.2 16.9 0.4
C2 A:TFA411 1.1 16.1 0.4
C2 A:TFA411 1.4 44.2 0.6
F2 A:TFA411 2.0 15.0 0.4
F3 A:TFA411 2.1 18.4 0.4
F2 A:TFA411 2.2 43.8 0.6
F3 A:TFA411 2.2 44.3 0.6
C1 A:TFA411 2.2 16.1 0.4
C1 A:TFA411 2.4 44.6 0.6
O A:TFA411 2.8 18.1 0.4
O A:TFA411 2.9 44.3 0.6
HA A:PHE253 2.9 8.1 1.0
HG23 A:VAL252 3.0 12.3 1.0
HD3 A:PRO254 3.0 9.9 1.0
O A:GLY241 3.1 12.0 1.0
OXT A:TFA411 3.3 14.4 0.4
OXT A:TFA411 3.3 44.8 0.6
O A:HOH2468 3.4 18.3 0.5
CA A:PHE253 3.5 6.8 1.0
C A:PHE253 3.5 6.6 1.0
HG3 A:PRO254 3.6 12.3 1.0
N A:PRO254 3.6 7.3 1.0
HG A:SER289 3.6 11.3 0.2
HG2 A:LYS243 3.7 18.0 1.0
CD A:PRO254 3.7 8.2 1.0
HA A:ALA242 3.7 10.2 1.0
HE2 A:LYS243 3.7 27.1 1.0
N A:PHE253 3.8 6.8 1.0
O A:HOH2468 3.8 29.0 0.5
O A:VAL252 3.9 8.0 1.0
CG2 A:VAL252 3.9 10.2 1.0
C A:VAL252 3.9 7.3 1.0
HG A:SER289 4.0 13.8 0.8
C A:GLY241 4.1 9.9 1.0
O A:PHE253 4.1 7.0 1.0
HA A:PRO254 4.1 9.4 1.0
CG A:PRO254 4.1 10.3 1.0
HG21 A:VAL252 4.1 12.3 1.0
H A:PHE253 4.2 8.1 1.0
HB A:VAL252 4.3 10.8 1.0
HD3 A:LYS243 4.3 23.1 1.0
CA A:PRO254 4.4 7.8 1.0
H A:LYS243 4.4 11.2 1.0
OG A:SER289 4.5 9.4 0.2
CA A:ALA242 4.5 8.5 1.0
HB3 A:SER289 4.5 11.5 0.8
CE A:LYS243 4.5 22.6 1.0
HD2 A:PRO254 4.5 9.9 1.0
CG A:LYS243 4.6 15.0 1.0
HA A:SER289 4.6 9.3 0.2
HG22 A:VAL252 4.6 12.3 1.0
HA A:SER289 4.6 9.4 0.8
CB A:VAL252 4.6 9.0 1.0
HZ3 A:LYS243 4.7 30.4 1.0
HA3 A:GLY241 4.7 12.9 1.0
N A:ALA242 4.7 8.4 1.0
CD A:LYS243 4.7 19.2 1.0
OG A:SER289 4.7 11.5 0.8
N A:LYS243 4.8 9.3 1.0
HB2 A:SER289 4.9 10.3 0.2
HG2 A:PRO254 4.9 12.3 1.0
CB A:PRO254 4.9 9.7 1.0
CA A:VAL252 4.9 7.7 1.0
CB A:PHE253 4.9 7.4 1.0
C A:ALA242 5.0 9.5 1.0
CA A:GLY241 5.0 10.8 1.0

Fluorine binding site 3 out of 6 in 5lwt

Go back to Fluorine Binding Sites List in 5lwt
Fluorine binding site 3 out of 6 in the Endothiapepsin in Complex with A Methoxylated 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 Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:15.0
occ:0.42
F2 A:TFA411 0.0 15.0 0.4
F2 A:TFA411 0.5 43.8 0.6
C2 A:TFA411 1.4 16.1 0.4
C2 A:TFA411 1.4 44.2 0.6
HG A:SER289 1.8 11.3 0.2
F1 A:TFA411 2.0 44.3 0.6
F1 A:TFA411 2.2 16.9 0.4
F3 A:TFA411 2.2 18.4 0.4
C1 A:TFA411 2.3 16.1 0.4
C1 A:TFA411 2.4 44.6 0.6
F3 A:TFA411 2.4 44.3 0.6
OXT A:TFA411 2.6 14.4 0.4
HG A:SER289 2.6 13.8 0.8
OG A:SER289 2.6 9.4 0.2
HB3 A:SER289 2.6 11.5 0.8
OXT A:TFA411 2.6 44.8 0.6
HA A:SER289 2.8 9.3 0.2
HA A:SER289 2.9 9.4 0.8
HG23 A:VAL252 2.9 12.3 1.0
HB A:VAL252 3.1 10.8 1.0
OG A:SER289 3.2 11.5 0.8
CB A:SER289 3.2 9.6 0.8
HB2 A:SER289 3.2 10.3 0.2
O A:PHE253 3.2 7.0 1.0
CB A:SER289 3.2 8.6 0.2
C A:PHE253 3.3 6.6 1.0
H A:PHE253 3.4 8.1 1.0
N A:PHE253 3.4 6.8 1.0
CA A:SER289 3.5 7.8 0.8
CA A:SER289 3.5 7.8 0.2
O A:TFA411 3.5 18.1 0.4
O A:TFA411 3.5 44.3 0.6
HG21 A:VAL252 3.5 12.3 1.0
CG2 A:VAL252 3.5 10.2 1.0
HA A:PHE253 3.6 8.1 1.0
H A:CYS290 3.6 8.2 1.0
CA A:PHE253 3.6 6.8 1.0
HA A:PRO254 3.7 9.4 1.0
CB A:VAL252 3.7 9.0 1.0
N A:PRO254 3.8 7.3 1.0
C A:VAL252 3.9 7.3 1.0
HB2 A:SER289 4.1 11.5 0.8
N A:CYS290 4.1 6.9 1.0
HB3 A:SER289 4.2 10.3 0.2
HD3 A:PRO254 4.2 9.9 1.0
C A:SER289 4.2 7.4 0.2
HE2 A:LYS243 4.3 27.1 1.0
C A:SER289 4.3 7.4 0.8
CA A:PRO254 4.3 7.8 1.0
O A:VAL252 4.4 8.0 1.0
HG22 A:VAL252 4.4 12.3 1.0
CA A:VAL252 4.4 7.7 1.0
CD A:PRO254 4.5 8.2 1.0
HG3 A:PRO254 4.6 12.3 1.0
N A:SER289 4.6 7.3 0.8
N A:SER289 4.7 7.7 0.2
O A:CYS290 4.7 8.1 1.0
O A:SER288 4.8 9.5 1.0
HG2 A:LYS243 4.8 18.0 1.0
HA A:VAL252 4.9 9.2 1.0
HG11 A:VAL252 5.0 12.2 1.0

Fluorine binding site 4 out of 6 in 5lwt

Go back to Fluorine Binding Sites List in 5lwt
Fluorine binding site 4 out of 6 in the Endothiapepsin in Complex with A Methoxylated 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 Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:43.8
occ:0.58
F2 A:TFA411 0.0 43.8 0.6
F2 A:TFA411 0.5 15.0 0.4
C2 A:TFA411 1.4 44.2 0.6
C2 A:TFA411 1.4 16.1 0.4
HG A:SER289 1.7 11.3 0.2
C1 A:TFA411 2.1 16.1 0.4
OXT A:TFA411 2.1 14.4 0.4
HG A:SER289 2.2 13.8 0.8
F3 A:TFA411 2.2 44.3 0.6
F1 A:TFA411 2.2 44.3 0.6
F3 A:TFA411 2.3 18.4 0.4
C1 A:TFA411 2.3 44.6 0.6
F1 A:TFA411 2.5 16.9 0.4
HB3 A:SER289 2.5 11.5 0.8
HA A:SER289 2.5 9.3 0.2
HA A:SER289 2.5 9.4 0.8
OG A:SER289 2.5 9.4 0.2
OXT A:TFA411 2.6 44.8 0.6
OG A:SER289 2.8 11.5 0.8
HB2 A:SER289 2.8 10.3 0.2
CB A:SER289 2.9 9.6 0.8
CB A:SER289 3.0 8.6 0.2
CA A:SER289 3.1 7.8 0.8
CA A:SER289 3.1 7.8 0.2
O A:PHE253 3.2 7.0 1.0
O A:TFA411 3.3 18.1 0.4
HG23 A:VAL252 3.4 12.3 1.0
C A:PHE253 3.4 6.6 1.0
HB A:VAL252 3.4 10.8 1.0
HA A:PRO254 3.5 9.4 1.0
O A:TFA411 3.5 44.3 0.6
H A:CYS290 3.5 8.2 1.0
H A:PHE253 3.7 8.1 1.0
N A:PHE253 3.8 6.8 1.0
N A:PRO254 3.8 7.3 1.0
HB2 A:SER289 3.8 11.5 0.8
HG21 A:VAL252 3.8 12.3 1.0
HA A:PHE253 3.9 8.1 1.0
HB3 A:SER289 3.9 10.3 0.2
CG2 A:VAL252 3.9 10.2 1.0
CA A:PHE253 3.9 6.8 1.0
C A:SER289 4.0 7.4 0.2
N A:CYS290 4.0 6.9 1.0
C A:SER289 4.1 7.4 0.8
CB A:VAL252 4.1 9.0 1.0
CA A:PRO254 4.1 7.8 1.0
N A:SER289 4.2 7.3 0.8
N A:SER289 4.3 7.7 0.2
C A:VAL252 4.3 7.3 1.0
HD3 A:PRO254 4.4 9.9 1.0
O A:SER288 4.4 9.5 1.0
HE2 A:LYS243 4.5 27.1 1.0
HG3 A:PRO254 4.5 12.3 1.0
CD A:PRO254 4.6 8.2 1.0
C A:SER288 4.7 7.9 1.0
H A:SER289 4.8 8.8 0.8
H A:SER289 4.8 9.2 0.2
O A:HOH2483 4.8 13.9 1.0
O A:VAL252 4.8 8.0 1.0
HG22 A:VAL252 4.8 12.3 1.0
CA A:VAL252 4.8 7.7 1.0
O A:CYS290 4.9 8.1 1.0
CG A:PRO254 5.0 10.3 1.0
H A:CYS255 5.0 9.7 1.0

Fluorine binding site 5 out of 6 in 5lwt

Go back to Fluorine Binding Sites List in 5lwt
Fluorine binding site 5 out of 6 in the Endothiapepsin in Complex with A Methoxylated 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 Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:18.4
occ:0.42
F3 A:TFA411 0.0 18.4 0.4
C1 A:TFA411 0.4 44.6 0.6
O A:TFA411 1.3 44.3 0.6
C2 A:TFA411 1.4 16.1 0.4
OXT A:TFA411 1.4 44.8 0.6
C2 A:TFA411 1.4 44.2 0.6
F1 A:TFA411 2.1 44.3 0.6
F2 A:TFA411 2.2 15.0 0.4
F1 A:TFA411 2.2 16.9 0.4
F2 A:TFA411 2.3 43.8 0.6
C1 A:TFA411 2.3 16.1 0.4
F3 A:TFA411 2.4 44.3 0.6
HE2 A:LYS243 2.6 27.1 1.0
HG A:SER289 3.0 13.8 0.8
O A:TFA411 3.0 18.1 0.4
OXT A:TFA411 3.1 14.4 0.4
HG A:SER289 3.2 11.3 0.2
HZ3 A:LYS243 3.2 30.4 1.0
HG23 A:VAL252 3.3 12.3 1.0
CE A:LYS243 3.4 22.6 1.0
HZ1 A:LYS243 3.5 30.4 1.0
OG A:SER289 3.6 11.5 0.8
NZ A:LYS243 3.6 25.3 1.0
HG21 A:VAL252 3.6 12.3 1.0
O A:HOH2468 3.6 18.3 0.5
OG A:SER289 3.8 9.4 0.2
HB2 A:SER289 3.8 10.3 0.2
HB3 A:SER289 3.9 11.5 0.8
CG2 A:VAL252 3.9 10.2 1.0
HG2 A:LYS243 3.9 18.0 1.0
HD3 A:LYS243 4.0 23.1 1.0
HE3 A:LYS243 4.1 27.1 1.0
CD A:LYS243 4.2 19.2 1.0
CB A:SER289 4.3 9.6 0.8
O A:HOH2468 4.3 29.0 0.5
CB A:SER289 4.3 8.6 0.2
HZ2 A:LYS243 4.5 30.4 1.0
HB A:VAL252 4.5 10.8 1.0
HA A:SER289 4.6 9.3 0.2
O A:GLY241 4.6 12.0 1.0
HG22 A:VAL252 4.6 12.3 1.0
CG A:LYS243 4.6 15.0 1.0
HA A:SER289 4.6 9.4 0.8
CB A:VAL252 4.8 9.0 1.0
HA A:PHE253 4.9 8.1 1.0
HG3 A:LYS243 5.0 18.0 1.0
HG3 A:PRO254 5.0 12.3 1.0

Fluorine binding site 6 out of 6 in 5lwt

Go back to Fluorine Binding Sites List in 5lwt
Fluorine binding site 6 out of 6 in the Endothiapepsin in Complex with A Methoxylated 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 Endothiapepsin in Complex with A Methoxylated Derivative of Fragment 177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F411

b:44.3
occ:0.58
F3 A:TFA411 0.0 44.3 0.6
C1 A:TFA411 0.2 16.1 0.4
O A:TFA411 1.1 18.1 0.4
OXT A:TFA411 1.4 14.4 0.4
C2 A:TFA411 1.4 44.2 0.6
C2 A:TFA411 1.6 16.1 0.4
F2 A:TFA411 2.2 43.8 0.6
F1 A:TFA411 2.2 44.3 0.6
F1 A:TFA411 2.3 16.9 0.4
C1 A:TFA411 2.4 44.6 0.6
F2 A:TFA411 2.4 15.0 0.4
F3 A:TFA411 2.4 18.4 0.4
O A:TFA411 2.9 44.3 0.6
HG A:SER289 2.9 13.8 0.8
HG3 A:PRO254 3.0 12.3 1.0
HA A:PRO254 3.1 9.4 1.0
OXT A:TFA411 3.3 44.8 0.6
O A:HOH2468 3.5 29.0 0.5
O A:HOH2483 3.5 13.9 1.0
CA A:PRO254 3.7 7.8 1.0
N A:PRO254 3.7 7.3 1.0
CG A:PRO254 3.7 10.3 1.0
HA A:SER289 3.8 9.3 0.2
HA A:SER289 3.8 9.4 0.8
OG A:SER289 3.8 11.5 0.8
O A:HOH2468 3.8 18.3 0.5
HD3 A:PRO254 3.8 9.9 1.0
HG A:SER289 3.9 11.3 0.2
HB3 A:PRO254 3.9 11.7 1.0
HB2 A:SER289 4.0 10.3 0.2
CD A:PRO254 4.0 8.2 1.0
CB A:PRO254 4.0 9.7 1.0
C A:PHE253 4.1 6.6 1.0
O A:PHE253 4.3 7.0 1.0
HB3 A:SER289 4.4 11.5 0.8
HA A:PHE253 4.5 8.1 1.0
CB A:SER289 4.5 9.6 0.8
O A:GLY241 4.5 12.0 1.0
OG A:SER289 4.5 9.4 0.2
CA A:SER289 4.5 7.8 0.8
CB A:SER289 4.5 8.6 0.2
CA A:SER289 4.5 7.8 0.2
HG2 A:PRO254 4.6 12.3 1.0
O A:SER288 4.6 9.5 1.0
CA A:PHE253 4.8 6.8 1.0
HG23 A:VAL252 4.9 12.3 1.0
HE2 A:LYS243 5.0 27.1 1.0
HD2 A:PRO254 5.0 9.9 1.0
HB2 A:PRO254 5.0 11.7 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

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