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Fluorine in PDB 3q96: B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor

Enzymatic activity of B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor

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

Protein crystallography data

The structure of B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor, PDB code: 3q96 was solved by M.D.Sintchak, K.Aertgeerts, J.Yano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.73 / 3.10
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.029, 94.029, 165.264, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 28.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor (pdb code 3q96). 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 Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor, PDB code: 3q96:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3q96

Go back to Fluorine Binding Sites List in 3q96
Fluorine binding site 1 out of 6 in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor


Mono view


Stereo pair view

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

b:32.6
occ:1.00
 F37 A:0NF1 0.0 32.6 1.0
C34 A:0NF1 1.3 31.5 1.0
F36 A:0NF1 2.2 32.1 1.0
F35 A:0NF1 2.2 31.6 1.0
C27 A:0NF1 2.3 30.3 1.0
C28 A:0NF1 2.6 29.8 1.0
C26 A:0NF1 3.6 29.1 1.0
CD2 A:LEU567 3.7 21.0 1.0
CG2 A:ILE572 3.9 20.1 1.0
C29 A:0NF1 4.0 29.6 1.0
CD2 A:HIS574 4.1 19.2 1.0
CG1 A:VAL504 4.4 25.6 1.0
CD1 A:LEU567 4.4 22.0 1.0
CG A:HIS574 4.5 19.3 1.0
NE2 A:HIS574 4.6 19.1 1.0
CA A:HIS574 4.6 19.8 1.0
CG A:LEU567 4.7 21.2 1.0
C25 A:0NF1 4.7 28.2 1.0
C38 A:0NF1 4.8 29.5 1.0
C30 A:0NF1 4.9 29.1 1.0
CB A:HIS574 4.9 19.5 1.0
C32 A:0NF1 5.0 29.5 1.0

Fluorine binding site 2 out of 6 in 3q96

Go back to Fluorine Binding Sites List in 3q96
Fluorine binding site 2 out of 6 in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor


Mono view


Stereo pair view

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

b:31.6
occ:1.00
 F35 A:0NF1 0.0 31.6 1.0
C34 A:0NF1 1.3 31.5 1.0
F36 A:0NF1 2.2 32.1 1.0
F37 A:0NF1 2.2 32.6 1.0
C27 A:0NF1 2.3 30.3 1.0
C26 A:0NF1 2.9 29.1 1.0
C28 A:0NF1 3.4 29.8 1.0
CD2 A:HIS574 3.4 19.2 1.0
NE2 A:HIS574 3.5 19.1 1.0
CA A:GLY593 3.7 22.4 1.0
C A:GLY593 3.9 22.5 1.0
N A:ASP594 4.2 22.9 1.0
C25 A:0NF1 4.2 28.2 1.0
CG2 A:ILE592 4.2 23.1 1.0
O A:GLY593 4.3 22.5 1.0
N A:GLY593 4.3 22.3 1.0
CG A:HIS574 4.4 19.3 1.0
O23 A:0NF1 4.5 25.5 1.0
CE1 A:HIS574 4.5 18.8 1.0
O A:ILE592 4.5 22.3 1.0
C29 A:0NF1 4.6 29.6 1.0
C A:ILE592 4.6 22.4 1.0
CD2 A:LEU567 4.6 21.0 1.0
CD1 A:LEU567 4.7 22.0 1.0
C30 A:0NF1 4.9 29.1 1.0
ND1 A:HIS574 5.0 19.2 1.0

Fluorine binding site 3 out of 6 in 3q96

Go back to Fluorine Binding Sites List in 3q96
Fluorine binding site 3 out of 6 in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor


Mono view


Stereo pair view

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

b:32.1
occ:1.00
 F36 A:0NF1 0.0 32.1 1.0
C34 A:0NF1 1.3 31.5 1.0
F37 A:0NF1 2.2 32.6 1.0
F35 A:0NF1 2.2 31.6 1.0
C27 A:0NF1 2.3 30.3 1.0
C26 A:0NF1 2.9 29.1 1.0
C28 A:0NF1 3.4 29.8 1.0
CD2 A:LEU505 3.7 23.1 1.0
CD2 A:LEU567 4.0 21.0 1.0
C25 A:0NF1 4.2 28.2 1.0
CG1 A:VAL504 4.4 25.6 1.0
C29 A:0NF1 4.6 29.6 1.0
CG2 A:THR508 4.6 21.0 1.0
O23 A:0NF1 4.6 25.5 1.0
CG A:LEU505 4.7 23.6 1.0
CG2 A:ILE513 4.7 18.9 1.0
C30 A:0NF1 4.9 29.1 1.0

Fluorine binding site 4 out of 6 in 3q96

Go back to Fluorine Binding Sites List in 3q96
Fluorine binding site 4 out of 6 in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor


Mono view


Stereo pair view

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

b:29.2
occ:1.00
 F37 B:0NF1 0.0 29.2 1.0
C34 B:0NF1 1.3 29.3 1.0
F36 B:0NF1 2.2 29.6 1.0
F35 B:0NF1 2.2 29.6 1.0
C27 B:0NF1 2.3 28.6 1.0
CD2 B:HIS574 3.1 26.7 1.0
C28 B:0NF1 3.1 28.1 1.0
C26 B:0NF1 3.2 27.7 1.0
NE2 B:HIS574 3.4 26.5 1.0
CD1 B:LEU567 4.1 22.4 1.0
CG B:HIS574 4.1 26.5 1.0
CA B:GLY593 4.2 31.7 1.0
C B:GLY593 4.3 32.2 1.0
C29 B:0NF1 4.4 27.8 1.0
C25 B:0NF1 4.4 27.2 1.0
CE1 B:HIS574 4.4 26.4 1.0
CG2 B:ILE592 4.6 30.2 1.0
O B:GLY593 4.6 32.2 1.0
CD2 B:LEU567 4.6 22.8 1.0
N B:ASP594 4.6 32.9 1.0
ND1 B:HIS574 4.8 26.4 1.0
N B:GLY593 4.8 31.1 1.0
C30 B:0NF1 4.9 27.6 1.0
O B:ILE592 4.9 30.6 1.0
CB B:HIS574 4.9 26.5 1.0

Fluorine binding site 5 out of 6 in 3q96

Go back to Fluorine Binding Sites List in 3q96
Fluorine binding site 5 out of 6 in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor


Mono view


Stereo pair view

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

b:29.6
occ:1.00
 F35 B:0NF1 0.0 29.6 1.0
C34 B:0NF1 1.3 29.3 1.0
F36 B:0NF1 2.2 29.6 1.0
F37 B:0NF1 2.2 29.2 1.0
C27 B:0NF1 2.4 28.6 1.0
C26 B:0NF1 2.8 27.7 1.0
C28 B:0NF1 3.6 28.1 1.0
CD2 B:LEU505 4.0 26.2 1.0
C25 B:0NF1 4.2 27.2 1.0
CD2 B:LEU567 4.3 22.8 1.0
O23 B:0NF1 4.5 26.8 1.0
O B:ILE592 4.5 30.6 1.0
CA B:GLY593 4.6 31.7 1.0
CG2 B:ILE513 4.6 21.3 1.0
C29 B:0NF1 4.7 27.8 1.0
CG1 B:VAL504 4.8 28.3 1.0
CD1 B:LEU567 4.9 22.4 1.0
CG1 B:ILE513 4.9 20.7 1.0
C30 B:0NF1 5.0 27.6 1.0

Fluorine binding site 6 out of 6 in 3q96

Go back to Fluorine Binding Sites List in 3q96
Fluorine binding site 6 out of 6 in the B-Raf Kinase Domain in Complex with A Tetrahydronaphthalene Inhibitor


Mono view


Stereo pair view

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

b:29.6
occ:1.00
 F36 B:0NF1 0.0 29.6 1.0
C34 B:0NF1 1.3 29.3 1.0
F37 B:0NF1 2.2 29.2 1.0
F35 B:0NF1 2.2 29.6 1.0
C27 B:0NF1 2.3 28.6 1.0
C28 B:0NF1 2.7 28.1 1.0
C26 B:0NF1 3.6 27.7 1.0
CG1 B:VAL504 3.7 28.3 1.0
CD2 B:LEU567 3.8 22.8 1.0
CG2 B:ILE572 3.8 26.1 1.0
C29 B:0NF1 4.1 27.8 1.0
CD1 B:LEU567 4.3 22.4 1.0
CG B:LEU567 4.6 22.8 1.0
C38 B:0NF1 4.7 27.4 1.0
C25 B:0NF1 4.7 27.2 1.0
CD2 B:HIS574 4.7 26.7 1.0
C30 B:0NF1 4.9 27.6 1.0

Reference:

A.E.Gould, R.Adams, S.Adhikari, K.Aertgeerts, R.Afroze, C.Blackburn, E.F.Calderwood, R.Chau, J.Chouitar, M.O.Duffey, D.B.England, C.Farrer, N.Forsyth, K.Garcia, J.Gaulin, P.D.Greenspan, R.Guo, S.J.Harrison, S.C.Huang, N.Iartchouk, D.Janowick, M.S.Kim, B.Kulkarni, S.P.Langston, J.X.Liu, L.T.Ma, S.Menon, H.Mizutani, E.Paske, C.C.Renou, M.Rezaei, R.S.Rowland, M.D.Sintchak, M.D.Smith, S.G.Stroud, M.Tregay, Y.Tian, O.P.Veiby, T.J.Vos, S.Vyskocil, J.Williams, T.Xu, J.J.Yang, J.Yano, H.Zeng, D.M.Zhang, Q.Zhang, K.M.Galvin. Design and Optimization of Potent and Orally Bioavailable Tetrahydronaphthalene Raf Inhibitors. J.Med.Chem. V. 54 1836 2011.
ISSN: ISSN 0022-2623
PubMed: 21341678
DOI: 10.1021/JM101479Y
Page generated: Sun Dec 13 11:53:38 2020

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