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Fluorine in PDB 8sv9: Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088

Enzymatic activity of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088

All present enzymatic activity of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088, PDB code: 8sv9 was solved by E.Schonbrunn, L.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.18 / 2.30
Space group C 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 112.06, 139.96, 87.45, 90, 90, 90
R / Rfree (%) 21 / 24.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 (pdb code 8sv9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088, PDB code: 8sv9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8sv9

Go back to Fluorine Binding Sites List in 8sv9
Fluorine binding site 1 out of 6 in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:50.2
occ:1.00
 F06 A:WXH301 0.0 50.2 1.0
C05 A:WXH301 1.4 44.7 1.0
F08 A:WXH301 2.3 45.5 1.0
F07 A:WXH301 2.3 44.8 1.0
C04 A:WXH301 2.4 41.4 1.0
N03 A:WXH301 2.7 48.4 1.0
N A:HIS24 3.3 44.1 1.0
O A:HIS24 3.3 48.5 1.0
C A:HIS24 3.3 49.7 1.0
NE2 A:GLN142 3.6 60.0 1.0
CA A:HIS24 3.6 46.6 1.0
N A:GLY25 3.8 57.0 1.0
C A:GLY23 3.9 48.7 1.0
C02 A:WXH301 4.1 39.6 1.0
CG2 A:VAL30 4.1 43.1 1.0
CA A:GLY23 4.3 44.6 1.0
CA A:GLY25 4.5 45.8 1.0
O A:GLY23 4.5 57.7 1.0
O01 A:WXH301 4.7 40.5 1.0
CD A:GLN142 4.8 65.8 1.0
C09 A:WXH301 5.0 43.9 1.0
O A:ALA28 5.0 41.4 1.0

Fluorine binding site 2 out of 6 in 8sv9

Go back to Fluorine Binding Sites List in 8sv9
Fluorine binding site 2 out of 6 in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:44.8
occ:1.00
 F07 A:WXH301 0.0 44.8 1.0
C05 A:WXH301 1.4 44.7 1.0
F08 A:WXH301 2.3 45.5 1.0
F06 A:WXH301 2.3 50.2 1.0
C04 A:WXH301 2.4 41.4 1.0
O A:HOH457 3.1 44.5 1.0
O A:HOH443 3.3 34.9 1.0
CA A:GLY25 3.5 45.8 1.0
OD2 A:ASP165 3.6 52.1 1.0
N A:GLY25 3.6 57.0 1.0
N03 A:WXH301 3.7 48.4 1.0
NE2 A:GLN142 3.8 60.0 1.0
C A:HIS24 3.8 49.7 1.0
O A:HIS24 3.9 48.5 1.0
CG A:ASP165 4.3 41.0 1.0
CB A:ALA28 4.5 34.2 1.0
OD1 A:ASP165 4.7 45.0 1.0
O A:ALA28 4.7 41.4 1.0
CA A:HIS24 4.7 46.6 1.0
C A:GLY25 4.7 45.7 1.0
O A:HOH410 4.8 47.0 1.0
C02 A:WXH301 4.8 39.6 1.0
O01 A:WXH301 4.9 40.5 1.0
OD1 A:ASN143 4.9 37.1 1.0

Fluorine binding site 3 out of 6 in 8sv9

Go back to Fluorine Binding Sites List in 8sv9
Fluorine binding site 3 out of 6 in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:45.5
occ:1.00
 F08 A:WXH301 0.0 45.5 1.0
C05 A:WXH301 1.4 44.7 1.0
F06 A:WXH301 2.3 50.2 1.0
F07 A:WXH301 2.3 44.8 1.0
C04 A:WXH301 2.4 41.4 1.0
N03 A:WXH301 2.8 48.4 1.0
CE A:LYS46 3.3 42.5 1.0
C02 A:WXH301 3.4 39.6 1.0
CG2 A:VAL30 3.4 43.1 1.0
CB A:ALA28 3.5 34.2 1.0
O01 A:WXH301 3.6 40.5 1.0
O A:HOH443 3.6 34.9 1.0
NZ A:LYS46 4.0 36.1 1.0
O A:ALA28 4.2 41.4 1.0
C A:ALA28 4.3 52.0 1.0
N A:GLY25 4.3 57.0 1.0
C A:HIS24 4.4 49.7 1.0
CA A:ALA28 4.5 46.3 1.0
C09 A:WXH301 4.6 43.9 1.0
CD A:LYS46 4.6 35.0 1.0
CA A:HIS24 4.6 46.6 1.0
O A:HOH457 4.6 44.5 1.0
N A:VAL29 4.7 47.2 1.0
OD2 A:ASP165 4.7 52.1 1.0
N A:HIS24 4.8 44.1 1.0
CG A:LYS46 4.8 34.5 1.0
CA A:GLY25 4.9 45.8 1.0
CB A:VAL30 4.9 44.1 1.0
O A:HIS24 4.9 48.5 1.0
CG A:ASP165 4.9 41.0 1.0
OD1 A:ASP165 4.9 45.0 1.0

Fluorine binding site 4 out of 6 in 8sv9

Go back to Fluorine Binding Sites List in 8sv9
Fluorine binding site 4 out of 6 in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:66.5
occ:1.00
 F06 B:WXH301 0.0 66.5 1.0
C05 B:WXH301 1.4 52.6 1.0
F08 B:WXH301 2.3 49.5 1.0
F07 B:WXH301 2.3 44.6 1.0
C04 B:WXH301 2.4 46.8 1.0
N03 B:WXH301 2.8 46.0 1.0
C B:HIS24 3.1 57.8 1.0
N B:HIS24 3.2 60.1 1.0
O B:HIS24 3.3 56.5 1.0
CA B:HIS24 3.4 60.1 1.0
N B:GLY25 3.4 59.2 1.0
NE2 B:GLN142 3.5 47.5 0.5
C B:GLY23 3.8 54.9 1.0
C02 B:WXH301 4.1 43.8 1.0
CA B:GLY25 4.1 53.1 1.0
O B:HOH426 4.2 45.5 1.0
CG2 B:VAL30 4.2 45.9 1.0
O B:GLY23 4.3 51.0 1.0
CA B:GLY23 4.4 54.3 1.0
O01 B:WXH301 4.6 53.8 1.0
O B:ALA28 4.7 50.8 1.0
CD B:GLN142 4.8 47.2 0.5
CB B:HIS24 5.0 56.3 1.0

Fluorine binding site 5 out of 6 in 8sv9

Go back to Fluorine Binding Sites List in 8sv9
Fluorine binding site 5 out of 6 in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:44.6
occ:1.00
 F07 B:WXH301 0.0 44.6 1.0
C05 B:WXH301 1.4 52.6 1.0
F08 B:WXH301 2.3 49.5 1.0
F06 B:WXH301 2.3 66.5 1.0
C04 B:WXH301 2.4 46.8 1.0
CA B:GLY25 3.4 53.1 1.0
N B:GLY25 3.4 59.2 1.0
N03 B:WXH301 3.7 46.0 1.0
C B:HIS24 3.9 57.8 1.0
OD2 B:ASP165 4.0 53.6 1.0
O B:HIS24 4.2 56.5 1.0
NE2 B:GLN142 4.2 47.5 0.5
CB B:ALA28 4.2 44.9 1.0
C B:GLY25 4.5 53.0 1.0
CG B:ASP165 4.5 45.4 1.0
O B:ALA28 4.5 50.8 1.0
O01 B:WXH301 4.7 53.8 1.0
C02 B:WXH301 4.7 43.8 1.0
CA B:HIS24 4.7 60.1 1.0
OD1 B:ASP165 4.7 43.2 1.0
NZ B:LYS46 5.0 39.6 1.0

Fluorine binding site 6 out of 6 in 8sv9

Go back to Fluorine Binding Sites List in 8sv9
Fluorine binding site 6 out of 6 in the Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of ULK1 Kinase Domain with Inhibitor Mr-2088 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:49.5
occ:1.00
 F08 B:WXH301 0.0 49.5 1.0
C05 B:WXH301 1.4 52.6 1.0
F06 B:WXH301 2.3 66.5 1.0
F07 B:WXH301 2.3 44.6 1.0
C04 B:WXH301 2.4 46.8 1.0
N03 B:WXH301 2.8 46.0 1.0
C02 B:WXH301 3.3 43.8 1.0
O01 B:WXH301 3.3 53.8 1.0
CG2 B:VAL30 3.4 45.9 1.0
CB B:ALA28 3.5 44.9 1.0
CE B:LYS46 3.7 37.1 1.0
NZ B:LYS46 3.9 39.6 1.0
CD B:LYS46 4.3 40.6 1.0
N B:GLY25 4.3 59.2 1.0
O B:ALA28 4.3 50.8 1.0
C B:ALA28 4.4 50.5 1.0
C09 B:WXH301 4.5 39.8 1.0
CA B:ALA28 4.5 53.1 1.0
C B:HIS24 4.5 57.8 1.0
CA B:HIS24 4.6 60.1 1.0
CG B:LYS46 4.7 46.4 1.0
N B:HIS24 4.8 60.1 1.0
CB B:VAL30 4.9 42.9 1.0
N B:VAL29 4.9 45.1 1.0
CA B:GLY25 4.9 53.1 1.0
C B:GLY23 5.0 54.9 1.0
O B:GLY23 5.0 51.0 1.0

Reference:

A.Morozova, S.C.Chan, S.Bayle, L.Sun, D.Grassie, A.Iermolaieva, M.N.Kalaga, S.Frydman, S.Sansil, E.Schonbrunn, D.Duckett, A.Monastyrskyi. Development of Potent and Selective ULK1/2 Inhibitors Based on 7-Azaindole Scaffold with Favorable in Vivo Properties. Eur.J.Med.Chem. V. 266 16101 2024.
ISSN: ISSN 0223-5234
PubMed: 38232465
DOI: 10.1016/J.EJMECH.2023.116101
Page generated: Wed Jul 16 08:19:38 2025

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