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Fluorine in PDB 3k5v: Structure of Abl Kinase in Complex with Imatinib and Gnf-2

Enzymatic activity of Structure of Abl Kinase in Complex with Imatinib and Gnf-2

All present enzymatic activity of Structure of Abl Kinase in Complex with Imatinib and Gnf-2:
2.7.10.2;

Protein crystallography data

The structure of Structure of Abl Kinase in Complex with Imatinib and Gnf-2, PDB code: 3k5v was solved by S.W.Cowan-Jacob, G.Fendrich, G.Rummel, A.Strauss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.95 / 1.74
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 42.070, 65.268, 66.259, 72.82, 80.25, 84.86
R / Rfree (%) 19.9 / 23.1

Other elements in 3k5v:

The structure of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2 (pdb code 3k5v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2, PDB code: 3k5v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3k5v

Go back to Fluorine Binding Sites List in 3k5v
Fluorine binding site 1 out of 6 in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:26.0
occ:1.00
 F1 A:STJ1 0.0 26.0 1.0
C2 A:STJ1 1.4 25.0 1.0
O5 A:STJ1 2.2 24.2 1.0
F4 A:STJ1 2.2 25.3 1.0
F3 A:STJ1 2.2 26.0 1.0
CB A:ALA363 3.4 14.7 1.0
C6 A:STJ1 3.5 23.3 1.0
CE1 A:PHE512 3.6 18.7 1.0
CD1 A:LEU448 3.7 17.9 1.0
CA A:LEU360 3.8 15.8 1.0
CD1 A:LEU360 3.8 18.6 1.0
CG1 A:VAL487 4.2 17.2 1.0
CZ A:PHE512 4.2 16.8 1.0
O A:LEU359 4.3 15.4 1.0
CB A:LEU360 4.3 16.4 1.0
N A:LEU360 4.3 15.9 1.0
C14 A:STJ1 4.4 25.6 1.0
CG2 A:VAL487 4.4 19.5 1.0
C7 A:STJ1 4.4 24.9 1.0
CD1 A:PHE512 4.4 21.1 1.0
O A:LEU360 4.6 15.0 1.0
C A:LEU359 4.6 16.0 1.0
C A:LEU360 4.7 15.3 1.0
CG A:LEU360 4.7 17.8 1.0
CG A:LEU448 4.9 17.8 1.0
CA A:ALA363 4.9 14.1 1.0
CD1 A:ILE521 4.9 23.2 1.0
CB A:VAL487 5.0 17.9 1.0

Fluorine binding site 2 out of 6 in 3k5v

Go back to Fluorine Binding Sites List in 3k5v
Fluorine binding site 2 out of 6 in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:26.0
occ:1.00
 F3 A:STJ1 0.0 26.0 1.0
C2 A:STJ1 1.4 25.0 1.0
F4 A:STJ1 2.2 25.3 1.0
F1 A:STJ1 2.2 26.0 1.0
O5 A:STJ1 2.3 24.2 1.0
C6 A:STJ1 2.9 23.3 1.0
C14 A:STJ1 3.1 25.6 1.0
CD1 A:LEU448 3.1 17.9 1.0
CG1 A:VAL487 3.7 17.2 1.0
CG2 A:ILE451 4.0 14.6 1.0
C7 A:STJ1 4.0 24.9 1.0
CG A:LEU448 4.0 17.8 1.0
O A:LEU448 4.1 14.0 1.0
C12 A:STJ1 4.3 25.8 1.0
CB A:ALA363 4.4 14.7 1.0
CB A:ALA452 4.5 16.1 1.0
N A:ALA452 4.5 14.8 1.0
CB A:ILE451 4.5 14.4 1.0
CA A:ALA452 4.7 16.0 1.0
O A:LEU359 4.8 15.4 1.0
CG2 A:VAL487 4.9 19.5 1.0
CB A:VAL487 4.9 17.9 1.0
C A:LEU448 4.9 14.3 1.0
C9 A:STJ1 5.0 25.0 1.0

Fluorine binding site 3 out of 6 in 3k5v

Go back to Fluorine Binding Sites List in 3k5v
Fluorine binding site 3 out of 6 in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:25.3
occ:1.00
 F4 A:STJ1 0.0 25.3 1.0
C2 A:STJ1 1.4 25.0 1.0
F1 A:STJ1 2.2 26.0 1.0
F3 A:STJ1 2.2 26.0 1.0
O5 A:STJ1 2.3 24.2 1.0
C6 A:STJ1 2.9 23.3 1.0
O A:LEU359 2.9 15.4 1.0
C A:LEU359 2.9 16.0 1.0
N A:LEU360 3.1 15.9 1.0
C7 A:STJ1 3.2 24.9 1.0
CA A:LEU360 3.3 15.8 1.0
CB A:LEU359 3.5 16.3 1.0
CG2 A:ILE451 3.5 14.6 1.0
CA A:LEU359 3.8 15.7 1.0
C14 A:STJ1 3.9 25.6 1.0
CB A:ALA363 4.0 14.7 1.0
CB A:LEU360 4.2 16.4 1.0
C9 A:STJ1 4.4 25.0 1.0
C A:LEU360 4.5 15.3 1.0
CD1 A:LEU448 4.7 17.9 1.0
O A:ALA356 4.7 18.4 1.0
CB A:ILE451 4.7 14.4 1.0
O A:LEU360 4.8 15.0 1.0
CG A:LEU359 4.8 17.7 1.0
C12 A:STJ1 4.9 25.8 1.0
CD1 A:LEU360 4.9 18.6 1.0
CD1 A:ILE521 5.0 23.2 1.0
N A:LEU359 5.0 15.0 1.0

Fluorine binding site 4 out of 6 in 3k5v

Go back to Fluorine Binding Sites List in 3k5v
Fluorine binding site 4 out of 6 in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:50.9
occ:1.00
 F1 B:STJ1 0.0 50.9 1.0
C2 B:STJ1 1.4 51.9 1.0
F3 B:STJ1 2.2 51.3 1.0
F4 B:STJ1 2.2 49.1 1.0
O5 B:STJ1 2.3 53.1 1.0
CE1 B:PHE512 3.6 43.3 1.0
C6 B:STJ1 3.6 55.3 1.0
CB B:ALA363 3.7 29.5 1.0
CA B:LEU360 3.7 34.2 1.0
CD1 B:LEU448 3.8 29.7 1.0
CD1 B:LEU360 3.9 34.4 1.0
CG1 B:VAL487 4.2 33.1 1.0
CB B:LEU360 4.2 34.6 1.0
CZ B:PHE512 4.2 42.6 1.0
N B:LEU360 4.3 34.5 1.0
CG2 B:VAL487 4.3 34.6 1.0
CD1 B:PHE512 4.3 44.0 1.0
O B:LEU359 4.3 34.6 1.0
C14 B:STJ1 4.4 56.3 1.0
C7 B:STJ1 4.5 56.3 1.0
C B:LEU359 4.5 35.1 1.0
O B:LEU360 4.7 33.6 1.0
C B:LEU360 4.7 33.8 1.0
CG B:LEU360 4.7 35.0 1.0
CB B:VAL487 4.9 33.3 1.0
CG B:LEU448 4.9 28.4 1.0
CD1 B:ILE521 5.0 59.9 1.0

Fluorine binding site 5 out of 6 in 3k5v

Go back to Fluorine Binding Sites List in 3k5v
Fluorine binding site 5 out of 6 in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:51.3
occ:1.00
 F3 B:STJ1 0.0 51.3 1.0
C2 B:STJ1 1.4 51.9 1.0
F4 B:STJ1 2.2 49.1 1.0
F1 B:STJ1 2.2 50.9 1.0
O5 B:STJ1 2.3 53.1 1.0
C6 B:STJ1 2.9 55.3 1.0
C14 B:STJ1 3.2 56.3 1.0
CD1 B:LEU448 3.2 29.7 1.0
CG1 B:VAL487 3.6 33.1 1.0
CG B:LEU448 4.0 28.4 1.0
C7 B:STJ1 4.0 56.3 1.0
CG2 B:ILE451 4.0 28.5 1.0
O B:LEU448 4.1 26.9 1.0
CB B:ALA452 4.4 30.1 1.0
C12 B:STJ1 4.4 57.1 1.0
N B:ALA452 4.5 30.1 1.0
CB B:ALA363 4.5 29.5 1.0
CB B:ILE451 4.6 28.1 1.0
CA B:ALA452 4.6 31.1 1.0
CG2 B:VAL487 4.7 34.6 1.0
CB B:VAL487 4.7 33.3 1.0
O B:LEU359 4.9 34.6 1.0
C B:LEU448 4.9 26.6 1.0
CD2 B:LEU448 5.0 27.9 1.0

Fluorine binding site 6 out of 6 in 3k5v

Go back to Fluorine Binding Sites List in 3k5v
Fluorine binding site 6 out of 6 in the Structure of Abl Kinase in Complex with Imatinib and Gnf-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Abl Kinase in Complex with Imatinib and Gnf-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1

b:49.1
occ:1.00
 F4 B:STJ1 0.0 49.1 1.0
C2 B:STJ1 1.4 51.9 1.0
F3 B:STJ1 2.2 51.3 1.0
F1 B:STJ1 2.2 50.9 1.0
O5 B:STJ1 2.3 53.1 1.0
C6 B:STJ1 2.9 55.3 1.0
C B:LEU359 3.0 35.1 1.0
O B:LEU359 3.0 34.6 1.0
N B:LEU360 3.1 34.5 1.0
C7 B:STJ1 3.3 56.3 1.0
CB B:LEU359 3.4 35.4 1.0
CA B:LEU360 3.4 34.2 1.0
CG2 B:ILE451 3.5 28.5 1.0
CA B:LEU359 3.8 35.3 1.0
C14 B:STJ1 3.9 56.3 1.0
CB B:ALA363 4.2 29.5 1.0
CB B:LEU360 4.3 34.6 1.0
C9 B:STJ1 4.4 57.2 1.0
C B:LEU360 4.6 33.8 1.0
CB B:ILE451 4.7 28.1 1.0
CG B:LEU359 4.7 35.2 1.0
O B:ALA356 4.7 43.2 1.0
CD1 B:LEU448 4.7 29.7 1.0
CD1 B:LEU359 4.9 35.4 1.0
C12 B:STJ1 4.9 57.1 1.0
N B:LEU359 5.0 36.4 1.0

Reference:

J.Zhang, F.J.Adrian, W.Jahnke, S.W.Cowan-Jacob, A.G.Li, R.E.Iacob, T.Sim, J.Powers, C.Dierks, F.Sun, G.R.Guo, Q.Ding, B.Okram, Y.Choi, A.Wojciechowski, X.Deng, G.Liu, G.Fendrich, A.Strauss, N.Vajpai, S.Grzesiek, T.Tuntland, Y.Liu, B.Bursulaya, M.Azam, P.W.Manley, J.R.Engen, G.Q.Daley, M.Warmuth, N.S.Gray. Targeting Bcr-Abl By Combining Allosteric with Atp-Binding-Site Inhibitors. Nature V. 463 501 2010.
ISSN: ISSN 0028-0836
PubMed: 20072125
DOI: 10.1038/NATURE08675
Page generated: Wed Jul 31 19:47:29 2024

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