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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

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