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Fluorine in PDB 3v5q: Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models

Enzymatic activity of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models

All present enzymatic activity of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models:
2.7.10.1;

Protein crystallography data

The structure of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models, PDB code: 3v5q was solved by A.Kreusch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.95 / 2.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 65.580, 65.580, 177.252, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 26.4

Other elements in 3v5q:

The structure of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models (pdb code 3v5q). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models, PDB code: 3v5q:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3v5q

Go back to Fluorine Binding Sites List in 3v5q
Fluorine binding site 1 out of 6 in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:39.0
occ:1.00
 F1 A:0F4902 0.0 39.0 1.0
C2 A:0F4902 1.3 36.0 1.0
F3 A:0F4902 2.1 42.9 1.0
F4 A:0F4902 2.1 38.0 1.0
C5 A:0F4902 2.3 35.9 1.0
C6 A:0F4902 2.8 35.2 1.0
C38 A:0F4902 3.6 36.3 1.0
CD2 A:LEU670 3.7 32.5 1.0
CD2 A:LEU595 3.7 40.3 1.0
CG2 A:ILE600 3.9 35.4 1.0
C7 A:0F4902 4.1 39.1 1.0
CD1 A:LEU670 4.3 27.3 1.0
CD1 A:ILE600 4.3 30.2 1.0
CE2 A:PHE675 4.3 34.0 1.0
CG A:LEU595 4.4 41.8 1.0
CG A:LEU670 4.5 33.5 1.0
CD2 A:HIS677 4.6 32.7 1.0
O A:ILE695 4.7 31.8 1.0
C9 A:0F4902 4.7 42.2 1.0
CD2 A:PHE675 4.8 32.8 1.0
CZ A:PHE675 4.8 33.8 1.0
CG2 A:ILE695 4.9 28.8 1.0
CG1 A:ILE600 4.9 33.4 1.0
CD2 A:LEU592 4.9 33.4 1.0
C8 A:0F4902 4.9 34.4 1.0
CB A:ILE600 5.0 34.3 1.0

Fluorine binding site 2 out of 6 in 3v5q

Go back to Fluorine Binding Sites List in 3v5q
Fluorine binding site 2 out of 6 in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:42.9
occ:1.00
 F3 A:0F4902 0.0 42.9 1.0
C2 A:0F4902 1.3 36.0 1.0
F1 A:0F4902 2.1 39.0 1.0
F4 A:0F4902 2.2 38.0 1.0
C5 A:0F4902 2.3 35.9 1.0
C38 A:0F4902 2.7 36.3 1.0
O A:ILE695 3.2 31.8 1.0
CG2 A:ILE600 3.3 35.4 1.0
CA A:GLY696 3.3 31.0 1.0
C6 A:0F4902 3.5 35.2 1.0
C A:GLY696 3.8 36.9 1.0
C A:ILE695 3.8 31.6 1.0
N A:GLY696 4.0 26.4 1.0
C9 A:0F4902 4.1 42.2 1.0
N A:ASP697 4.2 38.2 1.0
O A:GLY696 4.3 35.6 1.0
O12 A:0F4902 4.4 36.7 1.0
CD2 A:LEU592 4.5 33.4 1.0
CB A:ILE600 4.6 34.3 1.0
CD1 A:ILE600 4.7 30.2 1.0
C7 A:0F4902 4.7 39.1 1.0
N A:VAL601 4.7 30.6 1.0
CG2 A:ILE695 4.7 28.8 1.0
C8 A:0F4902 4.9 34.4 1.0
CA A:ILE600 4.9 31.2 1.0
CB A:ILE695 5.0 29.6 1.0
N10 A:0F4902 5.0 43.5 1.0

Fluorine binding site 3 out of 6 in 3v5q

Go back to Fluorine Binding Sites List in 3v5q
Fluorine binding site 3 out of 6 in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:38.0
occ:1.00
 F4 A:0F4902 0.0 38.0 1.0
C2 A:0F4902 1.3 36.0 1.0
F1 A:0F4902 2.1 39.0 1.0
F3 A:0F4902 2.2 42.9 1.0
C5 A:0F4902 2.3 35.9 1.0
C38 A:0F4902 3.1 36.3 1.0
O A:GLY696 3.1 35.6 1.0
C A:GLY696 3.2 36.9 1.0
C6 A:0F4902 3.2 35.2 1.0
CD2 A:HIS677 3.2 32.7 1.0
NE2 A:HIS677 3.3 33.5 1.0
CA A:GLY696 3.5 31.0 1.0
CG2 A:ILE695 3.6 28.8 1.0
N A:ASP697 3.7 38.2 1.0
CB A:ASP697 3.9 34.6 1.0
N A:GLY696 3.9 26.4 1.0
O A:ILE695 4.1 31.8 1.0
C A:ILE695 4.1 31.6 1.0
CA A:ASP697 4.3 39.5 1.0
C9 A:0F4902 4.4 42.2 1.0
C7 A:0F4902 4.4 39.1 1.0
CG A:HIS677 4.5 30.6 1.0
CE1 A:HIS677 4.6 35.0 1.0
CB A:ILE695 4.6 29.6 1.0
CD1 A:LEU670 4.7 27.3 1.0
CE2 A:PHE675 4.9 34.0 1.0
C8 A:0F4902 4.9 34.4 1.0
O12 A:0F4902 5.0 36.7 1.0
CG A:ASP697 5.0 39.4 1.0

Fluorine binding site 4 out of 6 in 3v5q

Go back to Fluorine Binding Sites List in 3v5q
Fluorine binding site 4 out of 6 in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:37.6
occ:1.00
 F1 B:0F4901 0.0 37.6 1.0
C2 B:0F4901 1.3 35.9 1.0
F3 B:0F4901 2.1 44.5 1.0
F4 B:0F4901 2.2 40.0 1.0
C5 B:0F4901 2.2 35.3 1.0
C6 B:0F4901 2.6 35.5 1.0
CD2 B:LEU595 3.2 39.8 1.0
C38 B:0F4901 3.5 33.8 1.0
CD2 B:LEU670 3.6 27.5 1.0
C7 B:0F4901 3.9 36.7 1.0
CG2 B:ILE600 3.9 32.5 1.0
CG B:LEU595 4.1 47.2 1.0
CD1 B:ILE600 4.3 32.5 1.0
CD1 B:LEU670 4.4 26.3 1.0
CE1 B:PHE675 4.5 34.4 1.0
CG B:LEU670 4.6 32.1 1.0
C9 B:0F4901 4.6 37.4 1.0
CD2 B:HIS677 4.7 29.3 1.0
C8 B:0F4901 4.7 36.7 1.0
CD2 B:LEU592 4.8 34.9 1.0
O B:ILE695 4.8 27.5 1.0
CD1 B:PHE675 4.8 31.9 1.0
CZ B:PHE675 4.8 33.2 1.0
CG1 B:ILE600 4.8 34.6 1.0

Fluorine binding site 5 out of 6 in 3v5q

Go back to Fluorine Binding Sites List in 3v5q
Fluorine binding site 5 out of 6 in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:44.5
occ:1.00
 F3 B:0F4901 0.0 44.5 1.0
C2 B:0F4901 1.3 35.9 1.0
F1 B:0F4901 2.1 37.6 1.0
F4 B:0F4901 2.2 40.0 1.0
C5 B:0F4901 2.3 35.3 1.0
C38 B:0F4901 2.8 33.8 1.0
CG2 B:ILE600 3.1 32.5 1.0
O B:ILE695 3.2 27.5 1.0
CA B:GLY696 3.5 32.2 1.0
C6 B:0F4901 3.5 35.5 1.0
C B:ILE695 3.9 35.5 1.0
C B:GLY696 4.0 37.9 1.0
N B:GLY696 4.1 29.8 1.0
C9 B:0F4901 4.2 37.4 1.0
N B:ASP697 4.4 36.2 1.0
CD1 B:ILE600 4.4 32.5 1.0
CB B:ILE600 4.4 32.6 1.0
CD2 B:LEU592 4.5 34.9 1.0
O12 B:0F4901 4.5 36.4 1.0
O B:GLY696 4.7 40.1 1.0
C7 B:0F4901 4.7 36.7 1.0
CG2 B:ILE695 4.7 30.6 1.0
N B:VAL601 4.7 29.0 1.0
CD2 B:LEU595 4.8 39.8 1.0
CG1 B:ILE600 4.9 34.6 1.0
CA B:ILE600 4.9 31.5 1.0
C8 B:0F4901 4.9 36.7 1.0
CB B:ILE695 5.0 30.9 1.0

Fluorine binding site 6 out of 6 in 3v5q

Go back to Fluorine Binding Sites List in 3v5q
Fluorine binding site 6 out of 6 in the Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Discovery of A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:40.0
occ:1.00
 F4 B:0F4901 0.0 40.0 1.0
C2 B:0F4901 1.3 35.9 1.0
F3 B:0F4901 2.2 44.5 1.0
F1 B:0F4901 2.2 37.6 1.0
C5 B:0F4901 2.3 35.3 1.0
C6 B:0F4901 3.1 35.5 1.0
C38 B:0F4901 3.1 33.8 1.0
C B:GLY696 3.2 37.9 1.0
O B:GLY696 3.3 40.1 1.0
CD2 B:HIS677 3.4 29.3 1.0
CA B:GLY696 3.4 32.2 1.0
NE2 B:HIS677 3.5 33.3 1.0
CG2 B:ILE695 3.6 30.6 1.0
N B:ASP697 3.7 36.2 1.0
N B:GLY696 3.9 29.8 1.0
O B:ILE695 4.0 27.5 1.0
C B:ILE695 4.1 35.5 1.0
CB B:ASP697 4.1 33.4 1.0
C7 B:0F4901 4.3 36.7 1.0
C9 B:0F4901 4.3 37.4 1.0
CA B:ASP697 4.4 38.7 1.0
CB B:ILE695 4.5 30.9 1.0
CG B:HIS677 4.7 30.7 1.0
CE1 B:HIS677 4.7 35.6 1.0
CD1 B:LEU670 4.8 26.3 1.0
C8 B:0F4901 4.8 36.7 1.0
CG2 B:ILE600 5.0 32.5 1.0
CA B:ILE695 5.0 27.0 1.0
O12 B:0F4901 5.0 36.4 1.0

Reference:

P.Albaugh, Y.Fan, Y.Mi, F.Sun, F.Adrian, N.Li, Y.Jia, Y.Sarkisova, A.Kreusch, T.Hood, M.Lu, G.Liu, S.Huang, Z.Liu, J.Loren, T.Tuntland, D.S.Karanewsky, H.M.Seidel, V.Molteni. Discovery of Gnf-5837, A Selective Trk Inhibitor with Efficacy in Rodent Cancer Tumor Models. Acs Med Chem Lett V. 3 140 2012.
ISSN: ISSN 1948-5875
PubMed: 24900443
DOI: 10.1021/ML200261D
Page generated: Mon Jul 14 19:49:31 2025

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