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Fluorine in PDB 5csw: B-Raf in Complex with Dabrafenib

Enzymatic activity of B-Raf in Complex with Dabrafenib

All present enzymatic activity of B-Raf in Complex with Dabrafenib:
2.7.11.1;

Protein crystallography data

The structure of B-Raf in Complex with Dabrafenib, PDB code: 5csw was solved by G.Bader, H.Stadtmuller, S.Steurer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.73 / 2.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.359, 48.095, 101.168, 90.00, 95.32, 90.00
R / Rfree (%) 21.7 / 28.2

Other elements in 5csw:

The structure of B-Raf in Complex with Dabrafenib also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the B-Raf in Complex with Dabrafenib (pdb code 5csw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the B-Raf in Complex with Dabrafenib, PDB code: 5csw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5csw

Go back to Fluorine Binding Sites List in 5csw
Fluorine binding site 1 out of 6 in the B-Raf in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of B-Raf in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:45.2
occ:1.00
 F39 A:P06801 0.0 45.2 1.0
C32 A:P06801 1.4 40.5 1.0
C31 A:P06801 2.4 40.3 1.0
C30 A:P06801 2.4 39.4 1.0
N40 A:P06801 2.7 38.4 1.0
C16 A:P06801 2.9 41.3 1.0
N A:ASP594 3.0 25.9 1.0
O A:HOH905 3.1 34.4 1.0
N15 A:P06801 3.1 44.5 1.0
CA A:ASP594 3.4 29.9 1.0
CB A:ASP594 3.5 29.7 1.0
C33 A:P06801 3.6 37.1 1.0
C35 A:P06801 3.7 37.0 1.0
CZ A:PHE583 3.9 38.6 1.0
C12 A:P06801 3.9 45.2 1.0
C A:GLY593 3.9 23.7 1.0
CE2 A:PHE583 3.9 36.5 1.0
OD1 A:ASP594 3.9 33.1 1.0
CD2 A:LEU514 4.1 22.2 1.0
C14 A:P06801 4.1 50.4 1.0
C37 A:P06801 4.1 31.6 1.0
S42 A:P06801 4.2 34.4 1.0
CG A:ASP594 4.3 30.5 1.0
CA A:GLY593 4.3 23.6 1.0
NZ A:LYS483 4.3 36.0 1.0
O55 A:P06801 4.4 28.1 1.0
C4 A:P06801 4.7 36.6 1.0
O54 A:P06801 4.7 36.9 1.0
C2 A:P06801 4.7 41.8 1.0
C26 A:P06801 4.7 45.8 1.0
C A:ASP594 4.8 32.6 1.0
O A:GLY593 4.9 24.5 1.0
S13 A:P06801 4.9 43.0 1.0

Fluorine binding site 2 out of 6 in 5csw

Go back to Fluorine Binding Sites List in 5csw
Fluorine binding site 2 out of 6 in the B-Raf in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of B-Raf in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:41.6
occ:1.00
 F52 A:P06801 0.0 41.6 1.0
C49 A:P06801 1.3 40.0 1.0
C50 A:P06801 2.4 38.9 1.0
C43 A:P06801 2.4 35.7 1.0
O54 A:P06801 2.6 36.9 1.0
S42 A:P06801 3.0 34.4 1.0
CD1 A:LEU505 3.1 14.6 1.0
CG2 A:ILE527 3.3 19.1 1.0
CG2 A:THR529 3.6 14.9 1.0
C47 A:P06801 3.6 38.8 1.0
C46 A:P06801 3.6 38.9 1.0
C33 A:P06801 3.6 37.1 1.0
N40 A:P06801 4.0 38.4 1.0
CD1 A:ILE527 4.0 27.4 1.0
CB A:ILE527 4.1 22.8 1.0
C44 A:P06801 4.1 41.5 1.0
O55 A:P06801 4.2 28.1 1.0
C31 A:P06801 4.3 40.3 1.0
CG A:LEU505 4.3 26.3 1.0
CD2 A:LEU505 4.3 21.6 1.0
CD A:LYS483 4.7 22.2 1.0
CG1 A:ILE527 4.7 24.9 1.0
C37 A:P06801 4.7 31.6 1.0
F53 A:P06801 4.7 31.6 1.0
CB A:LEU505 5.0 27.7 1.0

Fluorine binding site 3 out of 6 in 5csw

Go back to Fluorine Binding Sites List in 5csw
Fluorine binding site 3 out of 6 in the B-Raf in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of B-Raf in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F801

b:31.6
occ:1.00
 F53 A:P06801 0.0 31.6 1.0
C46 A:P06801 1.3 38.9 1.0
C44 A:P06801 2.4 41.5 1.0
C43 A:P06801 2.4 35.7 1.0
O55 A:P06801 2.7 28.1 1.0
S42 A:P06801 2.9 34.4 1.0
N40 A:P06801 3.1 38.4 1.0
CA A:GLY593 3.2 23.6 1.0
C47 A:P06801 3.6 38.8 1.0
C49 A:P06801 3.6 40.0 1.0
N A:ASP594 3.7 25.9 1.0
CE1 A:PHE595 3.7 49.2 1.0
C A:GLY593 3.8 23.7 1.0
CZ A:PHE595 3.8 42.8 1.0
CD1 A:PHE595 3.9 42.3 1.0
CE2 A:PHE595 4.1 39.5 1.0
C50 A:P06801 4.1 38.9 1.0
CG A:PHE595 4.2 41.8 1.0
CD2 A:LEU514 4.2 22.2 1.0
O A:ILE592 4.2 27.1 1.0
CD2 A:PHE595 4.3 38.8 1.0
CB A:LEU514 4.3 19.3 1.0
O54 A:P06801 4.3 36.9 1.0
C31 A:P06801 4.3 40.3 1.0
N A:GLY593 4.4 25.2 1.0
N A:PHE595 4.4 37.0 1.0
CA A:ASP594 4.7 29.9 1.0
F52 A:P06801 4.7 41.6 1.0
C A:ILE592 4.7 24.7 1.0
CG A:LEU514 4.7 22.6 1.0
O A:GLY593 4.8 24.5 1.0
CD2 A:LEU505 4.8 21.6 1.0

Fluorine binding site 4 out of 6 in 5csw

Go back to Fluorine Binding Sites List in 5csw
Fluorine binding site 4 out of 6 in the B-Raf in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of B-Raf in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:39.2
occ:1.00
 F39 B:P06801 0.0 39.2 1.0
C32 B:P06801 1.4 37.0 1.0
C31 B:P06801 2.4 43.1 1.0
C30 B:P06801 2.4 37.1 1.0
N40 B:P06801 2.8 40.1 1.0
C16 B:P06801 2.9 40.4 1.0
N B:ASP594 2.9 33.8 1.0
N15 B:P06801 3.0 40.8 1.0
O B:HOH906 3.1 36.3 1.0
CA B:ASP594 3.4 38.4 1.0
C33 B:P06801 3.7 48.6 1.0
CB B:ASP594 3.7 38.6 1.0
C35 B:P06801 3.7 41.4 1.0
C12 B:P06801 4.0 44.2 1.0
C B:GLY593 4.0 29.6 1.0
CZ B:PHE583 4.0 34.3 1.0
CE2 B:PHE583 4.0 31.5 1.0
C14 B:P06801 4.1 42.6 1.0
C37 B:P06801 4.1 46.5 1.0
OD1 B:ASP594 4.2 38.1 1.0
CA B:GLY593 4.3 26.1 1.0
NZ B:LYS483 4.3 22.9 1.0
S42 B:P06801 4.3 39.8 1.0
CD2 B:LEU514 4.4 13.9 1.0
CG B:ASP594 4.4 39.1 1.0
C26 B:P06801 4.6 31.8 1.0
O55 B:P06801 4.7 35.0 1.0
C4 B:P06801 4.8 40.9 1.0
C B:ASP594 4.8 41.3 1.0
C2 B:P06801 4.8 45.0 1.0
S13 B:P06801 4.9 45.8 1.0
O54 B:P06801 4.9 41.1 1.0
C17 B:P06801 5.0 41.6 1.0

Fluorine binding site 5 out of 6 in 5csw

Go back to Fluorine Binding Sites List in 5csw
Fluorine binding site 5 out of 6 in the B-Raf in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of B-Raf in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:41.5
occ:1.00
 F52 B:P06801 0.0 41.5 1.0
C49 B:P06801 1.3 38.5 1.0
C43 B:P06801 2.4 37.2 1.0
C50 B:P06801 2.4 39.2 1.0
O54 B:P06801 2.6 41.1 1.0
S42 B:P06801 3.0 39.8 1.0
CG2 B:ILE527 3.2 12.5 1.0
CD1 B:LEU505 3.3 17.3 1.0
CG2 B:THR529 3.3 23.0 1.0
C33 B:P06801 3.5 48.6 1.0
C46 B:P06801 3.6 34.9 1.0
C47 B:P06801 3.6 38.2 1.0
N40 B:P06801 4.0 40.1 1.0
C44 B:P06801 4.1 36.4 1.0
CB B:ILE527 4.1 15.2 1.0
C31 B:P06801 4.2 43.1 1.0
CD1 B:ILE527 4.2 11.5 1.0
O55 B:P06801 4.2 35.0 1.0
CG B:LEU505 4.5 21.9 1.0
C37 B:P06801 4.5 46.5 1.0
CD2 B:LEU505 4.6 15.5 1.0
F53 B:P06801 4.7 38.4 1.0
CB B:THR529 4.7 24.8 1.0
CG1 B:ILE527 4.8 13.1 1.0
CD B:LYS483 4.9 21.8 1.0

Fluorine binding site 6 out of 6 in 5csw

Go back to Fluorine Binding Sites List in 5csw
Fluorine binding site 6 out of 6 in the B-Raf in Complex with Dabrafenib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of B-Raf in Complex with Dabrafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F801

b:38.4
occ:1.00
 F53 B:P06801 0.0 38.4 1.0
C46 B:P06801 1.3 34.9 1.0
C43 B:P06801 2.3 37.2 1.0
C44 B:P06801 2.4 36.4 1.0
O55 B:P06801 2.6 35.0 1.0
S42 B:P06801 2.9 39.8 1.0
N40 B:P06801 3.1 40.1 1.0
CA B:GLY593 3.3 26.1 1.0
CD1 B:PHE595 3.5 52.3 1.0
CE1 B:PHE595 3.5 50.3 1.0
C49 B:P06801 3.6 38.5 1.0
C47 B:P06801 3.6 38.2 1.0
C B:GLY593 3.9 29.6 1.0
N B:ASP594 4.0 33.8 1.0
CG B:PHE595 4.0 50.4 1.0
CZ B:PHE595 4.0 47.7 1.0
C50 B:P06801 4.1 39.2 1.0
O B:ILE592 4.2 26.4 1.0
O54 B:P06801 4.3 41.1 1.0
C31 B:P06801 4.4 43.1 1.0
CD2 B:LEU514 4.4 13.9 1.0
CD2 B:PHE595 4.5 49.8 1.0
N B:PHE595 4.5 45.0 1.0
CE2 B:PHE595 4.5 47.4 1.0
CB B:LEU514 4.5 18.3 1.0
N B:GLY593 4.6 24.7 1.0
F52 B:P06801 4.7 41.5 1.0
CB B:PHE595 4.7 46.3 1.0
O B:GLY593 4.8 30.4 1.0
C B:ILE592 4.8 24.1 1.0
CA B:ASP594 5.0 38.4 1.0

Reference:

I.C.Waizenegger, A.Baum, S.Steurer, H.Stadtmuller, G.Bader, O.Schaaf, P.Garin-Chesa, A.Schlattl, N.Schweifer, C.Haslinger, F.Colbatzky, S.Mousa, A.Kalkuhl, N.Kraut, G.R.Adolf. A Novel Raf Kinase Inhibitor with Dfg-Out-Binding Mode: High Efficacy in Braf-Mutant Tumor Xenograft Models in the Absence of Normal Tissue Hyperproliferation. Mol.Cancer Ther. V. 15 354 2016.
ISSN: ESSN 1538-8514
PubMed: 26916115
DOI: 10.1158/1535-7163.MCT-15-0617
Page generated: Thu Aug 1 08:33:40 2024

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