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Fluorine in PDB 5fbn: Btk Kinase Domain with Inhibitor 1

Enzymatic activity of Btk Kinase Domain with Inhibitor 1

All present enzymatic activity of Btk Kinase Domain with Inhibitor 1:
2.7.10.2;

Protein crystallography data

The structure of Btk Kinase Domain with Inhibitor 1, PDB code: 5fbn was solved by H.C.A.Raaijmakers, D.Vu-Pham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.05 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.262, 71.475, 103.056, 90.00, 90.68, 90.00
R / Rfree (%) 17.9 / 22.6

Other elements in 5fbn:

The structure of Btk Kinase Domain with Inhibitor 1 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Btk Kinase Domain with Inhibitor 1 (pdb code 5fbn). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Btk Kinase Domain with Inhibitor 1, PDB code: 5fbn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5fbn

Go back to Fluorine Binding Sites List in 5fbn
Fluorine binding site 1 out of 6 in the Btk Kinase Domain with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Btk Kinase Domain with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:28.0
occ:1.00
F19 C:5WF701 0.0 28.0 1.0
C16 C:5WF701 1.4 26.2 1.0
F17 C:5WF701 2.2 29.1 1.0
F18 C:5WF701 2.2 29.8 1.0
C13 C:5WF701 2.4 23.5 1.0
C14 C:5WF701 2.8 20.8 1.0
CZ C:PHE442 3.2 30.6 1.0
CE1 C:PHE442 3.2 30.1 1.0
C12 C:5WF701 3.6 21.6 1.0
CD2 C:LEU542 3.6 29.1 1.0
CD1 C:ILE472 3.7 20.3 1.0
CG1 C:ILE472 3.7 19.1 1.0
CG2 C:ILE472 3.9 18.2 1.0
CD1 C:LEU542 4.1 29.0 1.0
C15 C:5WF701 4.2 19.8 1.0
CG C:LEU542 4.4 27.7 1.0
CB C:ILE472 4.4 18.5 1.0
CE2 C:PHE442 4.4 31.7 1.0
O8 C:5WF701 4.4 18.4 1.0
CD1 C:PHE442 4.5 30.3 1.0
CB C:ALA446 4.6 34.8 1.0
C11 C:5WF701 4.7 20.3 1.0
N10 C:5WF701 5.0 19.0 1.0
CE C:MET449 5.0 35.3 1.0

Fluorine binding site 2 out of 6 in 5fbn

Go back to Fluorine Binding Sites List in 5fbn
Fluorine binding site 2 out of 6 in the Btk Kinase Domain with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Btk Kinase Domain with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:29.8
occ:1.00
F18 C:5WF701 0.0 29.8 1.0
C16 C:5WF701 1.4 26.2 1.0
F19 C:5WF701 2.2 28.0 1.0
F17 C:5WF701 2.2 29.1 1.0
C13 C:5WF701 2.4 23.5 1.0
C14 C:5WF701 3.1 20.8 1.0
C12 C:5WF701 3.3 21.6 1.0
CE C:MET450 3.6 38.2 1.0
CG2 C:ILE472 3.7 18.2 1.0
CD1 C:LEU460 3.8 22.9 1.0
CD2 C:LEU460 4.0 22.1 1.0
CB C:ALA446 4.0 34.8 1.0
CA C:ALA446 4.3 35.0 1.0
C15 C:5WF701 4.4 19.8 1.0
CG C:LEU460 4.4 21.9 1.0
CD1 C:ILE472 4.5 20.3 1.0
C11 C:5WF701 4.5 20.3 1.0
O C:ALA446 4.7 33.7 1.0
CG1 C:ILE472 4.7 19.1 1.0
CE C:MET449 4.8 35.3 1.0
CB C:ILE472 4.8 18.5 1.0
CZ C:PHE442 4.8 30.6 1.0
CG1 C:VAL463 4.9 22.5 1.0
C C:ALA446 4.9 35.6 1.0
CB C:LEU460 4.9 21.7 1.0
N10 C:5WF701 5.0 19.0 1.0
CE1 C:PHE442 5.0 30.1 1.0

Fluorine binding site 3 out of 6 in 5fbn

Go back to Fluorine Binding Sites List in 5fbn
Fluorine binding site 3 out of 6 in the Btk Kinase Domain with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Btk Kinase Domain with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:29.1
occ:1.00
F17 C:5WF701 0.0 29.1 1.0
C16 C:5WF701 1.4 26.2 1.0
F19 C:5WF701 2.2 28.0 1.0
F18 C:5WF701 2.2 29.8 1.0
C13 C:5WF701 2.4 23.5 1.0
CE C:MET449 2.9 35.3 1.0
C12 C:5WF701 2.9 21.6 1.0
CD2 C:LEU542 3.3 29.1 1.0
C14 C:5WF701 3.7 20.8 1.0
CE1 C:PHE442 3.7 30.1 1.0
CA C:ALA446 3.7 35.0 1.0
SD C:MET449 3.8 34.0 1.0
CB C:ALA446 3.8 34.8 1.0
CZ C:PHE442 4.2 30.6 1.0
C11 C:5WF701 4.3 20.3 1.0
CG C:LEU542 4.4 27.7 1.0
N C:ALA446 4.5 34.2 1.0
CB C:MET449 4.6 34.2 1.0
CD1 C:PHE442 4.6 30.3 1.0
CG C:MET449 4.7 34.5 1.0
CD1 C:LEU542 4.8 29.0 1.0
C15 C:5WF701 4.8 19.8 1.0
C C:ALA446 4.8 35.6 1.0
O C:ALA446 4.9 33.7 1.0
CD1 C:LEU460 4.9 22.9 1.0

Fluorine binding site 4 out of 6 in 5fbn

Go back to Fluorine Binding Sites List in 5fbn
Fluorine binding site 4 out of 6 in the Btk Kinase Domain with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Btk Kinase Domain with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F702

b:31.6
occ:1.00
F19 D:5WF702 0.0 31.6 1.0
C16 D:5WF702 1.4 28.0 1.0
F18 D:5WF702 2.2 30.3 1.0
F17 D:5WF702 2.2 31.5 1.0
C13 D:5WF702 2.4 24.5 1.0
C14 D:5WF702 3.1 21.7 1.0
CE1 D:PHE442 3.2 36.6 1.0
CD2 D:LEU542 3.3 28.8 1.0
CZ D:PHE442 3.4 37.7 1.0
C12 D:5WF702 3.4 23.0 1.0
CD1 D:ILE472 3.5 20.0 1.0
CB D:ALA446 4.2 41.9 1.0
CE D:MET449 4.2 41.1 1.0
CD1 D:LEU542 4.3 28.8 1.0
CG D:LEU542 4.3 27.6 1.0
CD1 D:PHE442 4.4 36.1 1.0
C15 D:5WF702 4.4 20.4 1.0
CG2 D:ILE472 4.4 19.2 1.0
CG1 D:ILE472 4.5 20.4 1.0
CA D:ALA446 4.5 41.9 1.0
C11 D:5WF702 4.6 21.3 1.0
CE2 D:PHE442 4.7 38.4 1.0

Fluorine binding site 5 out of 6 in 5fbn

Go back to Fluorine Binding Sites List in 5fbn
Fluorine binding site 5 out of 6 in the Btk Kinase Domain with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Btk Kinase Domain with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F702

b:30.3
occ:1.00
F18 D:5WF702 0.0 30.3 1.0
C16 D:5WF702 1.3 28.0 1.0
F17 D:5WF702 2.2 31.5 1.0
F19 D:5WF702 2.2 31.6 1.0
C13 D:5WF702 2.4 24.5 1.0
C14 D:5WF702 2.9 21.7 1.0
CG2 D:ILE472 3.4 19.2 1.0
C12 D:5WF702 3.5 23.0 1.0
CD1 D:LEU460 3.6 26.0 1.0
CD2 D:LEU460 3.7 25.2 1.0
CG D:LEU460 4.2 24.8 1.0
CD1 D:ILE472 4.2 20.0 1.0
C15 D:5WF702 4.2 20.4 1.0
CB D:ALA446 4.5 41.9 1.0
CB D:ILE472 4.6 19.5 1.0
C11 D:5WF702 4.6 21.3 1.0
CG1 D:ILE472 4.6 20.4 1.0
CB D:LEU460 4.7 23.8 1.0
CG1 D:VAL463 4.7 24.6 1.0
CA D:ALA446 4.7 41.9 1.0
O8 D:5WF702 4.8 18.7 1.0
O D:ALA446 4.9 43.9 1.0
N10 D:5WF702 4.9 20.0 1.0

Fluorine binding site 6 out of 6 in 5fbn

Go back to Fluorine Binding Sites List in 5fbn
Fluorine binding site 6 out of 6 in the Btk Kinase Domain with Inhibitor 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Btk Kinase Domain with Inhibitor 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F702

b:31.5
occ:1.00
F17 D:5WF702 0.0 31.5 1.0
C16 D:5WF702 1.3 28.0 1.0
F18 D:5WF702 2.2 30.3 1.0
F19 D:5WF702 2.2 31.6 1.0
C13 D:5WF702 2.3 24.5 1.0
C12 D:5WF702 2.7 23.0 1.0
CE D:MET449 3.1 41.1 1.0
SD D:MET449 3.5 38.2 1.0
CB D:MET449 3.5 38.2 1.0
C14 D:5WF702 3.6 21.7 1.0
CA D:ALA446 3.7 41.9 1.0
CD1 D:LEU460 3.8 26.0 1.0
CG D:MET449 4.0 37.4 1.0
CB D:ALA446 4.1 41.9 1.0
C11 D:5WF702 4.1 21.3 1.0
O D:ALA446 4.2 43.9 1.0
CD2 D:LEU542 4.3 28.8 1.0
C D:ALA446 4.5 43.5 1.0
N D:ALA446 4.7 41.4 1.0
C15 D:5WF702 4.8 20.4 1.0
CA D:MET449 4.9 40.3 1.0
CD2 D:LEU460 4.9 25.2 1.0
CE1 D:PHE442 4.9 36.6 1.0
O D:GLU445 4.9 37.9 1.0
CG D:LEU460 4.9 24.8 1.0
N10 D:5WF702 4.9 20.0 1.0

Reference:

J.Liu, D.Guiadeen, A.Krikorian, X.Gao, J.Wang, S.B.Boga, A.B.Alhassan, Y.Yu, H.Vaccaro, S.Liu, C.Yang, H.Wu, A.Cooper, J.De Man, A.Kaptein, K.Maloney, V.Hornak, Y.D.Gao, T.O.Fischmann, H.Raaijmakers, D.Vu-Pham, J.Presland, M.Mansueto, Z.Xu, E.Leccese, J.Zhang-Hoover, I.Knemeyer, C.G.Garlisi, N.Bays, P.Stivers, P.E.Brandish, A.Hicks, R.Kim, J.A.Kozlowski. Discovery of 8-Amino-Imidazo[1,5-A]Pyrazines As Reversible Btk Inhibitors For the Treatment of Rheumatoid Arthritis. Acs Med.Chem.Lett. V. 7 198 2016.
ISSN: ISSN 1948-5875
PubMed: 26985298
DOI: 10.1021/ACSMEDCHEMLETT.5B00463
Page generated: Thu Aug 1 09:19:54 2024

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