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Fluorine in PDB 3efw: Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor

Enzymatic activity of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor

All present enzymatic activity of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor, PDB code: 3efw was solved by S.F.Bellon, V.Cee, P.Hughes, S.Geuns-Meyer, D.Whittington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.63 / 2.29
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 118.511, 125.448, 75.752, 90.00, 90.00, 90.00
R / Rfree (%) 25.8 / 29.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor (pdb code 3efw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor, PDB code: 3efw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3efw

Go back to Fluorine Binding Sites List in 3efw
Fluorine binding site 1 out of 6 in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:40.1
occ:1.00
 F2 A:AK8404 0.0 40.1 1.0
C25 A:AK8404 1.3 39.8 1.0
F3 A:AK8404 2.2 40.6 1.0
F1 A:AK8404 2.2 40.2 1.0
C23 A:AK8404 2.4 39.6 1.0
C24 A:AK8404 2.9 39.1 1.0
C22 A:AK8404 3.6 39.1 1.0
C19 A:AK8404 4.2 37.2 1.0
O1 A:SO4405 4.5 53.5 1.0
CB A:GLN177 4.8 55.9 1.0
C21 A:AK8404 4.8 39.5 1.0

Fluorine binding site 2 out of 6 in 3efw

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Fluorine binding site 2 out of 6 in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:40.6
occ:1.00
 F3 A:AK8404 0.0 40.6 1.0
C25 A:AK8404 1.3 39.8 1.0
F2 A:AK8404 2.2 40.1 1.0
F1 A:AK8404 2.2 40.2 1.0
C23 A:AK8404 2.4 39.6 1.0
C22 A:AK8404 3.2 39.1 1.0
N A:LEU178 3.2 55.2 1.0
C24 A:AK8404 3.2 39.1 1.0
CA A:LEU178 3.3 54.9 1.0
C A:GLN177 3.5 55.6 1.0
CB A:LEU178 3.7 54.8 1.0
O A:GLN177 3.7 55.6 1.0
CB A:GLN177 3.9 55.9 1.0
O A:VAL174 4.0 56.2 1.0
CD1 A:LEU178 4.1 54.8 1.0
CA A:GLN177 4.3 55.8 1.0
C21 A:AK8404 4.5 39.5 1.0
C19 A:AK8404 4.5 37.2 1.0
CB A:VAL174 4.5 56.0 1.0
CG A:LEU178 4.5 54.9 1.0
C A:LEU178 4.7 54.7 1.0
CB A:GLU181 4.8 53.8 1.0
C20 A:AK8404 5.0 38.4 1.0

Fluorine binding site 3 out of 6 in 3efw

Go back to Fluorine Binding Sites List in 3efw
Fluorine binding site 3 out of 6 in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F404

b:40.2
occ:1.00
 F1 A:AK8404 0.0 40.2 1.0
C25 A:AK8404 1.3 39.8 1.0
F2 A:AK8404 2.2 40.1 1.0
F3 A:AK8404 2.2 40.6 1.0
C23 A:AK8404 2.4 39.6 1.0
C22 A:AK8404 2.7 39.1 1.0
CB A:VAL174 3.3 56.0 1.0
CG1 A:VAL174 3.5 55.9 1.0
C24 A:AK8404 3.6 39.1 1.0
CG2 A:VAL174 3.9 55.8 1.0
C21 A:AK8404 4.1 39.5 1.0
O A:VAL174 4.3 56.2 1.0
CB A:GLN177 4.4 55.9 1.0
CA A:VAL174 4.5 56.0 1.0
C19 A:AK8404 4.8 37.2 1.0
N A:LEU178 4.8 55.2 1.0
C A:VAL174 4.9 56.2 1.0
C20 A:AK8404 4.9 38.4 1.0

Fluorine binding site 4 out of 6 in 3efw

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Fluorine binding site 4 out of 6 in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:38.4
occ:1.00
 F2 B:AK8404 0.0 38.4 1.0
C25 B:AK8404 1.3 37.2 1.0
F1 B:AK8404 2.1 37.5 1.0
F3 B:AK8404 2.2 37.6 1.0
C23 B:AK8404 2.4 37.4 1.0
C24 B:AK8404 2.9 36.7 1.0
OE1 B:GLU181 3.3 51.2 1.0
C22 B:AK8404 3.6 36.9 1.0
OE2 B:GLU181 3.7 50.0 1.0
NE2 B:GLN177 3.8 56.9 1.0
CD B:GLU181 3.8 50.7 1.0
C19 B:AK8404 4.2 36.0 1.0
O1 B:SO4405 4.3 52.0 1.0
CB B:GLN177 4.5 56.9 1.0
CD B:GLN177 4.7 57.0 1.0
C21 B:AK8404 4.7 37.1 1.0
C20 B:AK8404 5.0 36.8 1.0

Fluorine binding site 5 out of 6 in 3efw

Go back to Fluorine Binding Sites List in 3efw
Fluorine binding site 5 out of 6 in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:37.6
occ:1.00
 F3 B:AK8404 0.0 37.6 1.0
C25 B:AK8404 1.3 37.2 1.0
F1 B:AK8404 2.2 37.5 1.0
F2 B:AK8404 2.2 38.4 1.0
C23 B:AK8404 2.3 37.4 1.0
N B:LEU178 3.1 55.9 1.0
C24 B:AK8404 3.2 36.7 1.0
C22 B:AK8404 3.2 36.9 1.0
CA B:LEU178 3.3 55.3 1.0
OE1 B:GLU181 3.4 51.2 1.0
CB B:GLN177 3.4 56.9 1.0
C B:GLN177 3.6 56.4 1.0
CB B:LEU178 3.6 55.4 1.0
CD B:GLU181 3.8 50.7 1.0
CD1 B:LEU178 4.0 55.2 1.0
O B:VAL174 4.1 58.1 1.0
OE2 B:GLU181 4.1 50.0 1.0
O B:GLN177 4.1 56.4 1.0
CA B:GLN177 4.1 56.9 1.0
NE2 B:GLN177 4.3 56.9 1.0
C19 B:AK8404 4.4 36.0 1.0
C21 B:AK8404 4.4 37.1 1.0
CG B:LEU178 4.5 55.2 1.0
CG B:GLU181 4.5 50.6 1.0
CG B:GLN177 4.7 57.0 1.0
CB B:GLU181 4.7 50.7 1.0
CD B:GLN177 4.7 57.0 1.0
CB B:VAL174 4.8 57.9 1.0
C B:LEU178 4.8 54.9 1.0
C20 B:AK8404 4.9 36.8 1.0

Fluorine binding site 6 out of 6 in 3efw

Go back to Fluorine Binding Sites List in 3efw
Fluorine binding site 6 out of 6 in the Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Auroraa with Pyridyl-Pyrimidine Urea Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:37.5
occ:1.00
 F1 B:AK8404 0.0 37.5 1.0
C25 B:AK8404 1.3 37.2 1.0
F2 B:AK8404 2.1 38.4 1.0
F3 B:AK8404 2.2 37.6 1.0
C23 B:AK8404 2.4 37.4 1.0
C22 B:AK8404 2.8 36.9 1.0
CB B:VAL174 3.2 57.9 1.0
CG1 B:VAL174 3.4 58.0 1.0
C24 B:AK8404 3.6 36.7 1.0
O B:VAL174 4.0 58.1 1.0
NE2 B:GLN177 4.0 56.9 1.0
CG2 B:VAL174 4.0 58.0 1.0
CB B:GLN177 4.0 56.9 1.0
C21 B:AK8404 4.1 37.1 1.0
CD B:GLN177 4.3 57.0 1.0
CA B:VAL174 4.4 57.9 1.0
N B:LEU178 4.6 55.9 1.0
C B:VAL174 4.6 58.1 1.0
OE1 B:GLN177 4.7 57.3 1.0
CG B:GLN177 4.7 57.0 1.0
C19 B:AK8404 4.8 36.0 1.0
CB B:LEU178 4.9 55.4 1.0
C20 B:AK8404 5.0 36.8 1.0
OE1 B:GLU181 5.0 51.2 1.0

Reference:

V.J.Cee, A.C.Cheng, K.Romero, S.Bellon, C.Mohr, D.A.Whittington, A.Bak, J.Bready, S.Caenepeel, A.Coxon, H.L.Deak, J.Fretland, Y.Gu, B.L.Hodous, X.Huang, J.L.Kim, J.Lin, A.M.Long, H.Nguyen, P.R.Olivieri, V.F.Patel, L.Wang, Y.Zhou, P.Hughes, S.Geuns-Meyer. Pyridyl-Pyrimidine Benzimidazole Derivatives As Potent, Selective, and Orally Bioavailable Inhibitors of Tie-2 Kinase. Bioorg.Med.Chem.Lett. V. 19 424 2009.
ISSN: ISSN 0960-894X
PubMed: 19062275
DOI: 10.1016/J.BMCL.2008.11.056
Page generated: Mon Jul 14 16:05:56 2025

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