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Fluorine in PDB 3tv4: Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor

Enzymatic activity of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor

All present enzymatic activity of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor, PDB code: 3tv4 was solved by W.C.Voegtli, L.T.Selby, W.-I.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.40
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 107.966, 107.966, 153.142, 90.00, 90.00, 90.00
R / Rfree (%) 24.1 / 30.7

Other elements in 3tv4:

The structure of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor also contains other interesting chemical elements:

Bromine (Br) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor (pdb code 3tv4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor, PDB code: 3tv4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3tv4

Go back to Fluorine Binding Sites List in 3tv4
Fluorine binding site 1 out of 4 in the Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:31.1
occ:1.00
 F18 A:TV41 0.0 31.1 1.0
C17 A:TV41 1.3 29.9 1.0
C12 A:TV41 2.3 31.2 1.0
C16 A:TV41 2.4 28.7 1.0
N20 A:TV41 2.7 29.5 1.0
O11 A:TV41 2.7 35.7 1.0
C10 A:TV41 2.7 34.2 1.0
CD2 A:LEU514 3.1 33.2 1.0
N A:ASP594 3.2 59.3 1.0
C13 A:TV41 3.6 30.1 1.0
C15 A:TV41 3.6 27.7 1.0
N9 A:TV41 3.8 38.2 1.0
CA A:GLY593 3.8 56.5 1.0
C A:GLY593 4.0 57.9 1.0
CA A:ASP594 4.1 60.6 1.0
C14 A:TV41 4.1 28.8 1.0
CE1 A:PHE583 4.2 43.6 1.0
S21 A:TV41 4.4 31.4 1.0
CB A:ASP594 4.4 60.6 1.0
CZ A:PHE583 4.4 43.9 1.0
NZ A:LYS483 4.5 62.4 1.0
CG A:LEU514 4.5 33.9 1.0
F19 A:TV41 4.7 30.2 1.0
C26 A:TV41 4.9 32.4 1.0
C5 A:TV41 4.9 41.5 1.0
O22 A:TV41 4.9 30.6 1.0

Fluorine binding site 2 out of 4 in 3tv4

Go back to Fluorine Binding Sites List in 3tv4
Fluorine binding site 2 out of 4 in the Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:30.2
occ:1.00
 F19 A:TV41 0.0 30.2 1.0
C13 A:TV41 1.3 30.1 1.0
C14 A:TV41 2.4 28.8 1.0
C12 A:TV41 2.4 31.2 1.0
C10 A:TV41 2.9 34.2 1.0
N9 A:TV41 3.0 38.2 1.0
N A:LYS483 3.3 66.1 1.0
CB A:LYS483 3.4 66.9 1.0
C17 A:TV41 3.6 29.9 1.0
C15 A:TV41 3.6 27.7 1.0
OG1 A:THR529 3.7 47.7 1.0
C A:VAL482 3.7 65.1 1.0
O A:ILE527 3.8 53.2 1.0
CB A:ALA481 3.8 62.2 1.0
O11 A:TV41 3.9 35.7 1.0
CA A:LYS483 3.9 67.1 1.0
CG1 A:VAL471 3.9 75.4 1.0
C A:ALA481 4.0 62.9 1.0
N A:VAL482 4.0 63.6 1.0
C16 A:TV41 4.1 28.7 1.0
O A:ALA481 4.1 62.8 1.0
CA A:VAL482 4.1 64.3 1.0
C5 A:TV41 4.2 41.5 1.0
O A:VAL482 4.3 65.1 1.0
CG A:LYS483 4.5 66.0 1.0
CA A:ALA481 4.5 62.5 1.0
CD A:LYS483 4.5 64.2 1.0
CG2 A:THR529 4.6 48.0 1.0
F18 A:TV41 4.7 31.1 1.0
N A:THR529 4.7 49.0 1.0
CB A:THR529 4.7 48.1 1.0
C4 A:TV41 4.9 42.5 1.0
C A:ILE527 4.9 53.2 1.0

Fluorine binding site 3 out of 4 in 3tv4

Go back to Fluorine Binding Sites List in 3tv4
Fluorine binding site 3 out of 4 in the Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:39.6
occ:1.00
 F18 B:TV41 0.0 39.6 1.0
C17 B:TV41 1.3 38.4 1.0
C12 B:TV41 2.4 39.2 1.0
C16 B:TV41 2.4 37.1 1.0
N20 B:TV41 2.7 37.4 1.0
C10 B:TV41 2.7 41.4 1.0
O11 B:TV41 2.9 42.0 1.0
N B:ASP594 3.0 51.7 1.0
C13 B:TV41 3.6 38.2 1.0
C15 B:TV41 3.6 36.7 1.0
N9 B:TV41 3.7 44.0 1.0
CD2 B:LEU514 3.7 30.8 1.0
CA B:GLY593 3.8 49.6 1.0
CA B:ASP594 3.8 52.9 1.0
C B:GLY593 3.9 50.7 1.0
CB B:ASP594 4.0 53.0 1.0
C14 B:TV41 4.1 37.5 1.0
CE1 B:PHE583 4.2 49.2 1.0
CZ B:PHE583 4.3 49.5 1.0
S21 B:TV41 4.4 38.0 1.0
NZ B:LYS483 4.5 48.0 1.0
F19 B:TV41 4.7 37.8 1.0
C5 B:TV41 4.8 46.5 1.0
C25 B:TV41 4.9 37.5 1.0
C24 B:TV41 4.9 38.1 1.0

Fluorine binding site 4 out of 4 in 3tv4

Go back to Fluorine Binding Sites List in 3tv4
Fluorine binding site 4 out of 4 in the Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human B-Raf Kinase Domain in Complex with An Bromopyridine Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:37.8
occ:1.00
 F19 B:TV41 0.0 37.8 1.0
C13 B:TV41 1.3 38.2 1.0
C14 B:TV41 2.4 37.5 1.0
C12 B:TV41 2.4 39.2 1.0
C10 B:TV41 2.9 41.4 1.0
N9 B:TV41 3.1 44.0 1.0
CB B:LYS483 3.4 54.7 1.0
N B:LYS483 3.5 54.5 1.0
C15 B:TV41 3.6 36.7 1.0
C17 B:TV41 3.6 38.4 1.0
CB B:ALA481 3.7 51.5 1.0
OG1 B:THR529 3.7 39.6 1.0
CG1 B:VAL471 3.7 60.4 1.0
O11 B:TV41 3.7 42.0 1.0
C B:ALA481 3.9 52.2 1.0
O B:ILE527 3.9 40.3 1.0
CA B:LYS483 3.9 55.2 1.0
C B:VAL482 4.0 53.8 1.0
N B:VAL482 4.0 52.7 1.0
O B:ALA481 4.0 52.3 1.0
C16 B:TV41 4.1 37.1 1.0
C5 B:TV41 4.2 46.5 1.0
CA B:VAL482 4.3 53.3 1.0
CA B:ALA481 4.4 51.8 1.0
CD B:LYS483 4.5 50.2 1.0
CG B:LYS483 4.5 52.8 1.0
CG2 B:THR529 4.7 38.8 1.0
C4 B:TV41 4.7 46.9 1.0
O B:VAL482 4.7 54.0 1.0
F18 B:TV41 4.7 39.6 1.0
CB B:THR529 4.8 38.8 1.0
N B:THR529 4.8 38.9 1.0
CB B:VAL471 4.8 60.6 1.0
CE B:LYS483 5.0 49.0 1.0

Reference:

S.Wenglowsky, L.Ren, K.A.Ahrendt, E.R.Laird, I.Aliagas, B.Alicke, A.J.Buckmelter, E.F.Choo, V.Dinkel, B.Feng, S.L.Gloor, S.E.Gould, S.Gross, J.Gunzner-Toste, J.D.Hansen, G.Hatzivassiliou, B.Liu, K.Malesky, S.Mathieu, B.Newhouse, N.J.Raddatz, Y.Ran, S.Rana, N.Randolph, T.Risom, J.Rudolph, S.Savage, L.T.Selby, M.Shrag, K.Song, H.L.Sturgis, W.C.Voegtli, Z.Wen, B.S.Willis, R.D.Woessner, W.I.Wu, W.B.Young, J.Grina. Pyrazolopyridine Inhibitors of B-Raf(V600E). Part 1: the Development of Selective, Orally Bioavailable, and Efficacious Inhibitors. Acs Med Chem Lett V. 2 342 2011.
ISSN: ISSN 1948-5875
PubMed: 24900315
DOI: 10.1021/ML200025Q
Page generated: Mon Jul 14 19:30:47 2025

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