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Fluorine in PDB 3tv6: Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl Benzamide Inhibitor

Enzymatic activity of Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl Benzamide Inhibitor

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

Protein crystallography data

The structure of Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl Benzamide Inhibitor, PDB code: 3tv6 was solved by W.C.Voegtli, H.L.Sturgis, W.-I.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.75 / 3.30
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 108.440, 108.440, 150.700, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 28.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl Benzamide Inhibitor (pdb code 3tv6). 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 A Methoxypyrazolopyridinyl Benzamide Inhibitor, PDB code: 3tv6:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3tv6

Go back to Fluorine Binding Sites List in 3tv6
Fluorine binding site 1 out of 4 in the Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl 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 A Methoxypyrazolopyridinyl Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:36.2
occ:1.00
 F19 A:B0R1 0.0 36.2 1.0
C18 A:B0R1 1.4 35.6 1.0
C17 A:B0R1 2.4 34.2 1.0
C12 A:B0R1 2.4 36.6 1.0
C11 A:B0R1 3.0 39.0 1.0
N10 A:B0R1 3.1 42.0 1.0
N A:LYS483 3.4 66.8 1.0
CB A:LYS483 3.5 68.0 1.0
C14 A:B0R1 3.7 35.1 1.0
C16 A:B0R1 3.7 33.4 1.0
C A:VAL482 3.7 65.5 1.0
CB A:ALA481 3.7 61.7 1.0
OG1 A:THR529 3.8 50.0 1.0
C A:ALA481 3.8 62.6 1.0
O A:ALA481 3.9 62.5 1.0
O13 A:B0R1 3.9 40.1 1.0
N A:VAL482 3.9 63.7 1.0
CA A:LYS483 3.9 68.2 1.0
O A:ILE527 4.0 53.0 1.0
CA A:VAL482 4.1 64.7 1.0
CG2 A:VAL471 4.1 75.0 1.0
C15 A:B0R1 4.2 33.9 1.0
O A:VAL482 4.3 65.3 1.0
CG1 A:VAL471 4.3 75.2 1.0
C5 A:B0R1 4.3 45.2 1.0
CA A:ALA481 4.4 61.9 1.0
CG2 A:THR529 4.6 49.8 1.0
CG A:LYS483 4.7 67.1 1.0
CB A:VAL471 4.7 75.2 1.0
CD A:LYS483 4.7 65.6 1.0
CB A:THR529 4.8 50.1 1.0
F20 A:B0R1 4.8 36.4 1.0
N A:THR529 4.8 50.5 1.0

Fluorine binding site 2 out of 4 in 3tv6

Go back to Fluorine Binding Sites List in 3tv6
Fluorine binding site 2 out of 4 in the Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl 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 A Methoxypyrazolopyridinyl Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:36.4
occ:1.00
 F20 A:B0R1 0.0 36.4 1.0
C14 A:B0R1 1.3 35.1 1.0
C12 A:B0R1 2.4 36.6 1.0
C15 A:B0R1 2.4 33.9 1.0
N21 A:B0R1 2.7 33.8 1.0
C11 A:B0R1 2.7 39.0 1.0
O13 A:B0R1 2.8 40.1 1.0
CD2 A:LEU514 3.2 38.5 1.0
N A:ASP594 3.4 61.3 1.0
OD2 A:ASP594 3.5 64.5 1.0
CE1 A:PHE583 3.6 50.6 1.0
C18 A:B0R1 3.7 35.6 1.0
C16 A:B0R1 3.7 33.4 1.0
CA A:GLY593 3.7 59.0 1.0
N10 A:B0R1 3.7 42.0 1.0
CZ A:PHE583 3.8 51.0 1.0
C A:GLY593 3.9 60.1 1.0
C17 A:B0R1 4.2 34.2 1.0
CA A:ASP594 4.3 62.5 1.0
S22 A:B0R1 4.4 35.4 1.0
CG A:ASP594 4.5 63.5 1.0
NZ A:LYS483 4.6 65.2 1.0
CG A:LEU514 4.7 38.5 1.0
CB A:ASP594 4.7 62.5 1.0
CD1 A:PHE583 4.7 50.8 1.0
F19 A:B0R1 4.8 36.2 1.0
C5 A:B0R1 4.8 45.2 1.0
O27 A:B0R1 4.8 35.7 1.0
N A:GLY593 4.9 57.3 1.0

Fluorine binding site 3 out of 4 in 3tv6

Go back to Fluorine Binding Sites List in 3tv6
Fluorine binding site 3 out of 4 in the Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl 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 A Methoxypyrazolopyridinyl Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:36.4
occ:1.00
 F19 B:B0R1 0.0 36.4 1.0
C18 B:B0R1 1.4 36.1 1.0
C17 B:B0R1 2.4 34.7 1.0
C12 B:B0R1 2.4 37.3 1.0
C11 B:B0R1 3.0 39.2 1.0
N10 B:B0R1 3.0 41.5 1.0
N B:LYS483 3.5 53.7 1.0
CB B:ALA481 3.5 50.4 1.0
CB B:LYS483 3.5 54.3 1.0
C16 B:B0R1 3.7 34.1 1.0
C B:ALA481 3.7 51.1 1.0
C14 B:B0R1 3.7 36.6 1.0
CG1 B:VAL471 3.7 56.6 1.0
O B:ALA481 3.8 51.1 1.0
N B:VAL482 3.9 51.8 1.0
OG1 B:THR529 3.9 44.9 1.0
O13 B:B0R1 3.9 39.9 1.0
C B:VAL482 3.9 53.0 1.0
CA B:LYS483 4.0 54.5 1.0
O B:ILE527 4.1 45.4 1.0
C15 B:B0R1 4.2 34.9 1.0
CA B:ALA481 4.2 50.6 1.0
C5 B:B0R1 4.2 45.0 1.0
CA B:VAL482 4.2 52.5 1.0
CD B:LYS483 4.6 52.0 1.0
CG B:LYS483 4.7 53.3 1.0
CG2 B:THR529 4.7 44.0 1.0
CG2 B:VAL471 4.7 56.8 1.0
O B:VAL482 4.7 53.1 1.0
CB B:VAL471 4.7 56.9 1.0
F20 B:B0R1 4.8 38.3 1.0
CB B:THR529 4.9 44.4 1.0
C6 B:B0R1 4.9 46.2 1.0
N B:THR529 4.9 44.6 1.0

Fluorine binding site 4 out of 4 in 3tv6

Go back to Fluorine Binding Sites List in 3tv6
Fluorine binding site 4 out of 4 in the Human B-Raf Kinase Domain in Complex with A Methoxypyrazolopyridinyl 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 A Methoxypyrazolopyridinyl Benzamide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:38.3
occ:1.00
 F20 B:B0R1 0.0 38.3 1.0
C14 B:B0R1 1.4 36.6 1.0
C12 B:B0R1 2.4 37.3 1.0
C15 B:B0R1 2.4 34.9 1.0
C11 B:B0R1 2.7 39.2 1.0
O13 B:B0R1 2.7 39.9 1.0
N21 B:B0R1 2.7 33.5 1.0
N B:ASP594 3.3 46.7 1.0
CD2 B:LEU514 3.4 28.7 1.0
CE1 B:PHE583 3.5 44.6 1.0
CZ B:PHE583 3.6 44.5 1.0
C18 B:B0R1 3.7 36.1 1.0
C16 B:B0R1 3.7 34.1 1.0
N10 B:B0R1 3.7 41.5 1.0
CA B:GLY593 3.9 44.4 1.0
CA B:ASP594 4.0 47.8 1.0
C B:GLY593 4.0 45.6 1.0
CB B:ASP594 4.1 47.8 1.0
OD2 B:ASP594 4.1 49.8 1.0
C17 B:B0R1 4.2 34.7 1.0
S22 B:B0R1 4.4 33.0 1.0
CG B:ASP594 4.5 48.4 1.0
CD1 B:PHE583 4.6 45.0 1.0
NZ B:LYS483 4.7 51.9 1.0
C5 B:B0R1 4.7 45.0 1.0
C24 B:B0R1 4.8 28.7 1.0
CE2 B:PHE583 4.8 44.4 1.0
F19 B:B0R1 4.8 36.4 1.0
CG B:LEU514 4.8 29.4 1.0
O27 B:B0R1 4.9 33.3 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 19:30:56 2025

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