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Fluorine in PDB 3zos: Structure of the DDR1 Kinase Domain in Complex with Ponatinib

Enzymatic activity of Structure of the DDR1 Kinase Domain in Complex with Ponatinib

All present enzymatic activity of Structure of the DDR1 Kinase Domain in Complex with Ponatinib:
2.7.10.1;

Protein crystallography data

The structure of Structure of the DDR1 Kinase Domain in Complex with Ponatinib, PDB code: 3zos was solved by P.Canning, J.M.Elkins, S.Goubin, P.Mahajan, A.Bradley, D.Coutandin, F.Vondelft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.41 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.951, 61.733, 80.193, 90.00, 104.40, 90.00
R / Rfree (%) 20.6 / 23.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib (pdb code 3zos). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib, PDB code: 3zos:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 3zos

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Fluorine binding site 1 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:16.9
occ:1.00
 F1 A:0LI1000 0.0 16.9 1.0
C19 A:0LI1000 1.3 17.3 1.0
F3 A:0LI1000 2.2 15.8 1.0
F2 A:0LI1000 2.2 16.6 1.0
C17 A:0LI1000 2.3 16.6 1.0
C20 A:0LI1000 2.9 15.0 1.0
C16 A:0LI1000 2.9 15.3 1.0
CD1 A:LEU679 3.1 22.4 1.0
C18 A:0LI1000 3.5 16.3 1.0
CD2 A:LEU757 3.6 16.6 1.0
CG2 A:ILE684 3.7 17.7 1.0
CD1 A:LEU757 3.8 16.0 1.0
CG A:LEU757 4.2 15.6 1.0
C15 A:0LI1000 4.2 16.4 1.0
N3 A:0LI1000 4.3 14.6 1.0
CG A:LEU679 4.4 23.4 1.0
CD2 A:LEU679 4.5 23.8 1.0
C13 A:0LI1000 4.7 16.6 1.0
CD1 A:ILE684 4.8 18.8 1.0
C24 A:0LI1000 4.9 14.9 1.0
O A:ILE782 4.9 13.1 1.0
CD2 A:HIS764 5.0 11.7 1.0
CB A:ILE684 5.0 17.6 1.0
C14 A:0LI1000 5.0 16.5 1.0
C21 A:0LI1000 5.0 14.4 1.0
CG1 A:ILE684 5.0 17.7 1.0

Fluorine binding site 2 out of 9 in 3zos

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Fluorine binding site 2 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:16.6
occ:1.00
 F2 A:0LI1000 0.0 16.6 1.0
C19 A:0LI1000 1.3 17.3 1.0
F3 A:0LI1000 2.1 15.8 1.0
F1 A:0LI1000 2.2 16.9 1.0
C17 A:0LI1000 2.4 16.6 1.0
C18 A:0LI1000 2.7 16.3 1.0
O A:ILE782 3.0 13.1 1.0
CA A:ALA783 3.3 13.2 1.0
C A:ILE782 3.5 12.7 1.0
N A:ALA783 3.6 12.6 1.0
C A:ALA783 3.6 13.4 1.0
C16 A:0LI1000 3.7 15.3 1.0
CG2 A:ILE684 3.7 17.7 1.0
CG2 A:ILE685 3.7 18.6 1.0
O A:ALA783 4.0 12.6 1.0
N A:ASP784 4.1 14.6 1.0
C13 A:0LI1000 4.1 16.6 1.0
CG2 A:ILE782 4.2 12.7 1.0
O1 A:0LI1000 4.3 17.0 1.0
CD1 A:LEU679 4.4 22.4 1.0
C20 A:0LI1000 4.4 15.0 1.0
CB A:ILE782 4.4 12.4 1.0
CA A:ILE782 4.6 12.8 1.0
CB A:ALA783 4.6 13.7 1.0
N A:ILE685 4.7 17.8 1.0
C15 A:0LI1000 4.8 16.4 1.0
CB A:ILE685 4.9 18.6 1.0
NE2 A:HIS764 4.9 11.3 1.0
CB A:ILE684 4.9 17.6 1.0
C14 A:0LI1000 5.0 16.5 1.0
N2 A:0LI1000 5.0 17.3 1.0
CB A:ASP784 5.0 16.5 1.0

Fluorine binding site 3 out of 9 in 3zos

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Fluorine binding site 3 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:15.8
occ:1.00
 F3 A:0LI1000 0.0 15.8 1.0
C19 A:0LI1000 1.3 17.3 1.0
F2 A:0LI1000 2.1 16.6 1.0
F1 A:0LI1000 2.2 16.9 1.0
C17 A:0LI1000 2.3 16.6 1.0
C16 A:0LI1000 3.0 15.3 1.0
C20 A:0LI1000 3.2 15.0 1.0
CD2 A:HIS764 3.2 11.7 1.0
NE2 A:HIS764 3.3 11.3 1.0
C18 A:0LI1000 3.3 16.3 1.0
O A:ALA783 3.6 12.6 1.0
C A:ALA783 3.8 13.4 1.0
CB A:ASP784 4.0 16.5 1.0
CG2 A:ILE782 4.0 12.7 1.0
C24 A:0LI1000 4.0 14.9 1.0
N3 A:0LI1000 4.1 14.6 1.0
CD1 A:LEU757 4.1 16.0 1.0
N A:ASP784 4.2 14.6 1.0
CA A:ALA783 4.2 13.2 1.0
C15 A:0LI1000 4.2 16.4 1.0
CG A:HIS764 4.3 11.2 1.0
CE1 A:HIS764 4.3 11.8 1.0
N A:ALA783 4.4 12.6 1.0
C13 A:0LI1000 4.5 16.6 1.0
C A:ILE782 4.7 12.7 1.0
CA A:ASP784 4.7 15.4 1.0
O A:ILE782 4.7 13.1 1.0
ND1 A:HIS764 4.8 11.5 1.0
C14 A:0LI1000 4.8 16.5 1.0
CB A:ILE782 4.9 12.4 1.0

Fluorine binding site 4 out of 9 in 3zos

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Fluorine binding site 4 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:28.4
occ:1.00
 F1 A:0LI1004 0.0 28.4 1.0
C19 A:0LI1004 1.4 25.3 1.0
C17 A:0LI1004 2.3 22.5 1.0
F2 A:0LI1004 2.3 24.4 1.0
F3 A:0LI1004 2.3 22.6 1.0
C16 A:0LI1004 2.9 21.9 1.0
CD1 B:LEU805 3.1 18.6 1.0
C20 A:0LI1004 3.1 20.7 1.0
C18 A:0LI1004 3.3 22.5 1.0
CD2 B:LEU805 3.5 17.3 1.0
C24 A:0LI1004 3.5 18.8 1.0
N3 A:0LI1004 3.7 18.4 1.0
CG B:LEU805 3.9 18.2 1.0
C15 A:0LI1004 4.1 21.1 1.0
CE1 B:PHE820 4.2 17.3 1.0
CA B:GLY818 4.3 21.5 1.0
CZ B:PHE820 4.3 16.9 1.0
O B:CYS814 4.5 15.7 1.0
C13 A:0LI1004 4.5 21.4 1.0
CE B:MET810 4.7 14.8 1.0
C14 A:0LI1004 4.8 21.4 1.0
C21 A:0LI1004 4.8 19.6 1.0

Fluorine binding site 5 out of 9 in 3zos

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Fluorine binding site 5 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:24.4
occ:1.00
 F2 A:0LI1004 0.0 24.4 1.0
C19 A:0LI1004 1.4 25.3 1.0
F1 A:0LI1004 2.3 28.4 1.0
C17 A:0LI1004 2.3 22.5 1.0
F3 A:0LI1004 2.3 22.6 1.0
C18 A:0LI1004 2.6 22.5 1.0
CE1 B:PHE820 3.5 17.3 1.0
CG2 A:VAL799 3.5 18.8 1.0
C16 A:0LI1004 3.6 21.9 1.0
CD2 B:LEU805 3.8 17.3 1.0
CZ B:PHE820 4.0 16.9 1.0
C13 A:0LI1004 4.0 21.4 1.0
CB A:GLN800 4.0 19.2 1.0
O1 A:0LI1004 4.1 23.8 1.0
C20 A:0LI1004 4.4 20.7 1.0
CD1 B:PHE820 4.6 17.1 1.0
CB A:ALA803 4.6 18.0 1.0
CG A:GLN800 4.6 20.0 1.0
C15 A:0LI1004 4.7 21.1 1.0
CD1 B:LEU805 4.7 18.6 1.0
CB A:VAL799 4.7 18.7 1.0
OE1 A:GLN800 4.8 19.0 1.0
C14 A:0LI1004 4.8 21.4 1.0
CG B:LEU805 4.9 18.2 1.0
N2 A:0LI1004 4.9 21.7 1.0
C12 A:0LI1004 4.9 23.1 1.0
CD1 A:LEU805 4.9 16.6 1.0
CA B:GLY818 5.0 21.5 1.0

Fluorine binding site 6 out of 9 in 3zos

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Fluorine binding site 6 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1004

b:22.6
occ:1.00
 F3 A:0LI1004 0.0 22.6 1.0
C19 A:0LI1004 1.4 25.3 1.0
F1 A:0LI1004 2.3 28.4 1.0
F2 A:0LI1004 2.3 24.4 1.0
C17 A:0LI1004 2.3 22.5 1.0
C16 A:0LI1004 2.9 21.9 1.0
C20 A:0LI1004 2.9 20.7 1.0
C18 A:0LI1004 3.5 22.5 1.0
CD2 B:LEU805 3.5 17.3 1.0
CD1 B:LEU805 3.7 18.6 1.0
CD1 A:LEU805 4.0 16.6 1.0
CB A:ALA803 4.0 18.0 1.0
CG B:LEU805 4.0 18.2 1.0
CG2 A:VAL799 4.0 18.8 1.0
C15 A:0LI1004 4.1 21.1 1.0
N3 A:0LI1004 4.3 18.4 1.0
CD2 A:LEU805 4.3 16.0 1.0
CB B:ALA803 4.3 21.5 1.0
CG A:LEU805 4.3 16.5 1.0
C13 A:0LI1004 4.6 21.4 1.0
C24 A:0LI1004 4.8 18.8 1.0
C14 A:0LI1004 4.8 21.4 1.0

Fluorine binding site 7 out of 9 in 3zos

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Fluorine binding site 7 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:13.9
occ:1.00
 F1 B:0LI1000 0.0 13.9 1.0
C19 B:0LI1000 1.3 15.3 1.0
F3 B:0LI1000 2.1 15.2 1.0
F2 B:0LI1000 2.3 14.9 1.0
C17 B:0LI1000 2.4 14.0 1.0
C20 B:0LI1000 3.0 13.1 1.0
C16 B:0LI1000 3.0 13.7 1.0
CD1 B:LEU679 3.2 17.4 1.0
CD2 B:LEU757 3.5 13.5 1.0
C18 B:0LI1000 3.5 13.7 1.0
CG2 B:ILE684 3.7 15.3 1.0
CD1 B:LEU757 3.8 12.0 1.0
CG B:LEU757 4.1 12.0 1.0
C15 B:0LI1000 4.3 13.3 1.0
CG B:LEU679 4.4 18.2 1.0
N3 B:0LI1000 4.4 12.5 1.0
CD2 B:LEU679 4.4 18.6 1.0
CD1 B:ILE684 4.7 16.8 1.0
C13 B:0LI1000 4.8 13.1 1.0
CG1 B:ILE684 4.9 16.1 1.0
CB B:ILE684 4.9 15.5 1.0
O B:ILE782 4.9 12.5 1.0
CD2 B:HIS764 5.0 9.9 1.0

Fluorine binding site 8 out of 9 in 3zos

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Fluorine binding site 8 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:14.9
occ:1.00
 F2 B:0LI1000 0.0 14.9 1.0
C19 B:0LI1000 1.4 15.3 1.0
F3 B:0LI1000 2.1 15.2 1.0
F1 B:0LI1000 2.3 13.9 1.0
C17 B:0LI1000 2.4 14.0 1.0
C18 B:0LI1000 2.7 13.7 1.0
O B:ILE782 3.0 12.5 1.0
CA B:ALA783 3.3 12.9 1.0
C B:ILE782 3.4 12.9 1.0
N B:ALA783 3.6 12.3 1.0
CG2 B:ILE684 3.6 15.3 1.0
C16 B:0LI1000 3.7 13.7 1.0
CG2 B:ILE685 3.7 17.1 1.0
C B:ALA783 3.7 12.9 1.0
O B:ALA783 4.1 12.1 1.0
C13 B:0LI1000 4.1 13.1 1.0
O1 B:0LI1000 4.2 15.1 1.0
N B:ASP784 4.2 13.8 1.0
CG2 B:ILE782 4.2 12.7 1.0
CD1 B:LEU679 4.3 17.4 1.0
C20 B:0LI1000 4.5 13.1 1.0
CB B:ILE782 4.5 12.4 1.0
CA B:ILE782 4.6 12.6 1.0
N B:ILE685 4.6 15.9 1.0
CB B:ALA783 4.6 13.5 1.0
CB B:ILE684 4.8 15.5 1.0
CB B:ILE685 4.8 17.3 1.0
C15 B:0LI1000 4.8 13.3 1.0
N2 B:0LI1000 4.9 14.0 1.0
C12 B:0LI1000 5.0 14.8 1.0

Fluorine binding site 9 out of 9 in 3zos

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Fluorine binding site 9 out of 9 in the Structure of the DDR1 Kinase Domain in Complex with Ponatinib


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of the DDR1 Kinase Domain in Complex with Ponatinib within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1000

b:15.2
occ:1.00
 F3 B:0LI1000 0.0 15.2 1.0
C19 B:0LI1000 1.3 15.3 1.0
F1 B:0LI1000 2.1 13.9 1.0
F2 B:0LI1000 2.1 14.9 1.0
C17 B:0LI1000 2.3 14.0 1.0
C16 B:0LI1000 3.1 13.7 1.0
C20 B:0LI1000 3.3 13.1 1.0
CD2 B:HIS764 3.3 9.9 1.0
C18 B:0LI1000 3.3 13.7 1.0
NE2 B:HIS764 3.3 10.4 1.0
O B:ALA783 3.6 12.1 1.0
C B:ALA783 3.8 12.9 1.0
CG2 B:ILE782 3.9 12.7 1.0
CB B:ASP784 4.1 15.0 1.0
CD1 B:LEU757 4.1 12.0 1.0
CA B:ALA783 4.2 12.9 1.0
N B:ASP784 4.2 13.8 1.0
C24 B:0LI1000 4.3 13.1 1.0
N B:ALA783 4.3 12.3 1.0
N3 B:0LI1000 4.3 12.5 1.0
C15 B:0LI1000 4.3 13.3 1.0
CG B:HIS764 4.4 10.0 1.0
CE1 B:HIS764 4.4 10.6 1.0
C B:ILE782 4.5 12.9 1.0
C13 B:0LI1000 4.5 13.1 1.0
O B:ILE782 4.6 12.5 1.0
CB B:ILE782 4.7 12.4 1.0
CA B:ASP784 4.7 14.3 1.0
CD2 B:LEU757 4.9 13.5 1.0
C14 B:0LI1000 5.0 13.2 1.0
ND1 B:HIS764 5.0 10.4 1.0

Reference:

P.Canning, J.M.Elkins, S.Goubin, P.Mahajan, A.Bradley, D.Coutandin, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.Bullock. Structural Mechanisms Determining Inhibition of the Collagen Receptor DDR1 By Selective and Multi-Targeted Type II Kinase Inhibitors J.Mol.Biol. V. 426 2457 2014.
ISSN: ISSN 0022-2836
PubMed: 24768818
DOI: 10.1016/J.JMB.2014.04.014
Page generated: Wed Jul 31 23:47:42 2024

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