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Fluorine in PDB 3ii5: The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor

Enzymatic activity of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor

All present enzymatic activity of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor:
2.7.11.1;

Protein crystallography data

The structure of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor, PDB code: 3ii5 was solved by W.Xu, D.Breger, N.Torres, M.Dutia, D.Powell, G.Ciszewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.55 / 2.79
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.219, 110.219, 148.468, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 25.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor (pdb code 3ii5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor, PDB code: 3ii5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ii5

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Fluorine binding site 1 out of 6 in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:40.2
occ:1.00
 F1 A:8311 0.0 40.2 1.0
C29 A:8311 1.4 42.2 1.0
F3 A:8311 2.2 41.5 1.0
F2 A:8311 2.2 45.6 1.0
C27 A:8311 2.4 41.9 1.0
C28 A:8311 2.7 38.9 1.0
CA A:GLY592 3.2 31.7 1.0
C A:GLY592 3.5 31.9 1.0
C26 A:8311 3.6 41.9 1.0
O A:ILE591 3.8 32.1 1.0
N A:GLY592 3.8 29.7 1.0
O A:GLY592 3.9 30.0 1.0
C A:ILE591 4.0 30.0 1.0
N A:ASP593 4.0 30.3 1.0
NE2 A:HIS573 4.0 34.2 1.0
CD2 A:HIS573 4.1 30.6 1.0
C23 A:8311 4.1 35.4 1.0
CG2 A:ILE591 4.1 27.0 1.0
CD1 A:LEU566 4.5 34.1 1.0
CG2 A:ILE512 4.6 29.5 1.0
O1 A:8311 4.6 35.8 1.0
C25 A:8311 4.7 38.0 1.0
CB A:ILE591 4.9 30.4 1.0
C22 A:8311 4.9 32.7 1.0
C24 A:8311 4.9 33.8 1.0

Fluorine binding site 2 out of 6 in 3ii5

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Fluorine binding site 2 out of 6 in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:45.6
occ:1.00
 F2 A:8311 0.0 45.6 1.0
C29 A:8311 1.4 42.2 1.0
F3 A:8311 2.2 41.5 1.0
F1 A:8311 2.2 40.2 1.0
C27 A:8311 2.4 41.9 1.0
C26 A:8311 2.9 41.9 1.0
C28 A:8311 3.6 38.9 1.0
CD2 A:HIS573 3.7 30.6 1.0
CD1 A:LEU566 3.7 34.1 1.0
NE2 A:HIS573 4.1 34.2 1.0
C25 A:8311 4.2 38.0 1.0
CG A:HIS573 4.3 33.7 1.0
CD2 A:LEU566 4.6 30.7 1.0
CG2 A:ILE571 4.7 30.3 1.0
C23 A:8311 4.8 35.4 1.0
CG A:LEU566 4.8 35.5 1.0
CE1 A:HIS573 4.9 34.4 1.0
CB A:HIS573 4.9 34.0 1.0
CA A:HIS573 5.0 31.4 1.0

Fluorine binding site 3 out of 6 in 3ii5

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Fluorine binding site 3 out of 6 in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:41.5
occ:1.00
 F3 A:8311 0.0 41.5 1.0
C29 A:8311 1.4 42.2 1.0
F2 A:8311 2.2 45.6 1.0
F1 A:8311 2.2 40.2 1.0
C27 A:8311 2.4 41.9 1.0
C28 A:8311 3.2 38.9 1.0
C26 A:8311 3.3 41.9 1.0
CG2 A:ILE512 3.9 29.5 1.0
CD2 A:LEU504 4.2 32.5 1.0
CD2 A:LEU566 4.2 30.7 1.0
CD1 A:LEU566 4.3 34.1 1.0
CG2 A:THR507 4.4 30.4 1.0
C23 A:8311 4.5 35.4 1.0
C25 A:8311 4.5 38.0 1.0
CG A:LEU566 4.9 35.5 1.0

Fluorine binding site 4 out of 6 in 3ii5

Go back to Fluorine Binding Sites List in 3ii5
Fluorine binding site 4 out of 6 in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:39.5
occ:1.00
 F1 B:8311 0.0 39.5 1.0
C29 B:8311 1.4 39.6 1.0
F3 B:8311 2.2 37.8 1.0
F2 B:8311 2.2 40.4 1.0
C27 B:8311 2.4 36.0 1.0
C28 B:8311 2.8 36.5 1.0
C B:GLY592 3.5 40.9 1.0
CA B:GLY592 3.6 35.8 1.0
C26 B:8311 3.6 34.7 1.0
O B:ILE591 3.6 36.1 1.0
O B:GLY592 3.8 41.0 1.0
NE2 B:HIS573 3.8 31.8 1.0
N B:ASP593 3.9 37.7 1.0
C B:ILE591 4.0 34.2 1.0
CD2 B:HIS573 4.0 29.5 1.0
N B:GLY592 4.0 35.5 1.0
C23 B:8311 4.1 36.2 1.0
CG2 B:ILE591 4.2 30.8 1.0
CB B:ASP593 4.6 39.5 1.0
C25 B:8311 4.7 40.5 1.0
CD1 B:LEU566 4.7 26.0 1.0
O1 B:8311 4.8 42.6 1.0
CA B:ASP593 4.8 36.0 1.0
CB B:ILE591 4.9 32.6 1.0
CE1 B:HIS573 4.9 32.5 1.0
C24 B:8311 4.9 36.0 1.0
CG2 B:ILE512 5.0 30.3 1.0

Fluorine binding site 5 out of 6 in 3ii5

Go back to Fluorine Binding Sites List in 3ii5
Fluorine binding site 5 out of 6 in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:40.4
occ:1.00
 F2 B:8311 0.0 40.4 1.0
C29 B:8311 1.4 39.6 1.0
F3 B:8311 2.2 37.8 1.0
F1 B:8311 2.2 39.5 1.0
C27 B:8311 2.4 36.0 1.0
C26 B:8311 2.8 34.7 1.0
C28 B:8311 3.6 36.5 1.0
CD1 B:LEU566 3.9 26.0 1.0
CD2 B:HIS573 4.0 29.5 1.0
C25 B:8311 4.2 40.5 1.0
NE2 B:HIS573 4.4 31.8 1.0
CD2 B:LEU566 4.4 28.3 1.0
CG2 B:ILE571 4.7 30.6 1.0
CG B:HIS573 4.7 27.8 1.0
C23 B:8311 4.8 36.2 1.0
CG B:LEU566 4.8 29.2 1.0

Fluorine binding site 6 out of 6 in 3ii5

Go back to Fluorine Binding Sites List in 3ii5
Fluorine binding site 6 out of 6 in the The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Complex of Wild-Type B-Raf with Pyrazolo Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:37.8
occ:1.00
 F3 B:8311 0.0 37.8 1.0
C29 B:8311 1.4 39.6 1.0
F1 B:8311 2.2 39.5 1.0
F2 B:8311 2.2 40.4 1.0
C27 B:8311 2.4 36.0 1.0
C28 B:8311 3.1 36.5 1.0
C26 B:8311 3.4 34.7 1.0
CD2 B:LEU504 3.7 35.5 1.0
CG2 B:ILE512 3.8 30.3 1.0
CD2 B:LEU566 4.3 28.3 1.0
C23 B:8311 4.4 36.2 1.0
O B:ILE591 4.5 36.1 1.0
C25 B:8311 4.6 40.5 1.0
CG2 B:THR507 4.7 37.9 1.0
CD1 B:LEU566 4.7 26.0 1.0
CG1 B:ILE512 4.9 28.9 1.0
CB B:ILE512 5.0 30.1 1.0
C24 B:8311 5.0 36.0 1.0

Reference:

D.M.Berger, N.Torres, M.Dutia, D.Powell, G.Ciszewski, A.Gopalsamy, J.I.Levin, K.H.Kim, W.Xu, J.Wilhelm, Y.Hu, K.Collins, L.Feldberg, S.Kim, E.Frommer, D.Wojciechowicz, R.Mallon. Non-Hinge-Binding Pyrazolo[1,5-A]Pyrimidines As Potent B-Raf Kinase Inhibitors. Bioorg.Med.Chem.Lett. V. 19 6519 2009.
ISSN: ISSN 0960-894X
PubMed: 19864136
DOI: 10.1016/J.BMCL.2009.10.049
Page generated: Wed Jul 31 19:31:53 2024

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