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Fluorine in PDB 6gwr: Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2

Enzymatic activity of Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2

All present enzymatic activity of Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2:
2.7.10.1;

Protein crystallography data

The structure of Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2, PDB code: 6gwr was solved by D.M.Pinkas, A.E.Fox, K.Kupinska, N.A.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, C.Bountra, A.N.Bullock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.70 / 2.07
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.200, 118.750, 61.430, 90.00, 92.05, 90.00
R / Rfree (%) 20.1 / 23.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 (pdb code 6gwr). 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 the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2, PDB code: 6gwr:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6gwr

Go back to Fluorine Binding Sites List in 6gwr
Fluorine binding site 1 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2


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 Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:28.4
occ:1.00
 F25 A:FEW1001 0.0 28.4 1.0
C24 A:FEW1001 1.4 28.5 1.0
F26 A:FEW1001 2.2 29.9 1.0
F27 A:FEW1001 2.3 26.8 1.0
C23 A:FEW1001 2.3 31.0 1.0
C28 A:FEW1001 2.7 27.9 1.0
CD1 A:LEU679 3.3 31.4 1.0
C22 A:FEW1001 3.6 28.4 1.0
CG2 A:ILE685 3.9 27.8 1.0
CG2 A:ILE684 3.9 24.4 1.0
O A:ILE782 4.0 22.3 1.0
C11 A:FEW1001 4.1 30.5 1.0
CA A:ALA783 4.3 23.3 1.0
C A:ALA783 4.5 23.6 1.0
O A:HOH1154 4.6 31.1 1.0
C A:ILE782 4.7 21.7 1.0
C13 A:FEW1001 4.7 29.4 1.0
O09 A:FEW1001 4.7 31.6 1.0
CG A:LEU679 4.7 28.6 1.0
N A:ASP784 4.8 27.2 1.0
N A:ALA783 4.9 23.6 1.0
O A:ILE685 4.9 26.4 1.0
C12 A:FEW1001 4.9 31.3 1.0
O A:ALA783 5.0 24.7 1.0

Fluorine binding site 2 out of 6 in 6gwr

Go back to Fluorine Binding Sites List in 6gwr
Fluorine binding site 2 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2


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 Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:29.9
occ:1.00
 F26 A:FEW1001 0.0 29.9 1.0
C24 A:FEW1001 1.4 28.5 1.0
F25 A:FEW1001 2.2 28.4 1.0
F27 A:FEW1001 2.3 26.8 1.0
C23 A:FEW1001 2.3 31.0 1.0
C28 A:FEW1001 3.1 27.9 1.0
NE2 A:HIS764 3.1 22.8 1.0
C A:ALA783 3.2 23.6 1.0
O A:ALA783 3.2 24.7 1.0
C22 A:FEW1001 3.3 28.4 1.0
CD2 A:HIS764 3.4 23.3 1.0
CB A:ASP784 3.4 30.5 1.0
N A:ASP784 3.6 27.2 1.0
CA A:ALA783 3.7 23.3 1.0
CA A:ASP784 4.1 27.3 1.0
CE1 A:HIS764 4.2 27.9 1.0
N A:ALA783 4.2 23.6 1.0
O A:ILE782 4.3 22.3 1.0
C11 A:FEW1001 4.4 30.5 1.0
CG2 A:ILE782 4.5 23.6 1.0
O A:HOH1162 4.5 30.7 1.0
C A:ILE782 4.5 21.7 1.0
C13 A:FEW1001 4.5 29.4 1.0
CG A:HIS764 4.5 20.8 1.0
CG A:ASP784 4.7 28.3 1.0
OD2 A:ASP784 4.8 31.7 1.0
O09 A:FEW1001 4.8 31.6 1.0
ND1 A:HIS764 4.9 24.9 1.0
C12 A:FEW1001 4.9 31.3 1.0

Fluorine binding site 3 out of 6 in 6gwr

Go back to Fluorine Binding Sites List in 6gwr
Fluorine binding site 3 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2


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 Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:26.8
occ:1.00
 F27 A:FEW1001 0.0 26.8 1.0
C24 A:FEW1001 1.4 28.5 1.0
F26 A:FEW1001 2.3 29.9 1.0
F25 A:FEW1001 2.3 28.4 1.0
C23 A:FEW1001 2.4 31.0 1.0
C22 A:FEW1001 2.8 28.4 1.0
CD1 A:LEU679 3.3 31.4 1.0
CE1 A:PHE762 3.4 29.4 1.0
CZ A:PHE762 3.5 33.0 1.0
C28 A:FEW1001 3.6 27.9 1.0
C13 A:FEW1001 4.1 29.4 1.0
O A:HOH1162 4.2 30.7 1.0
CD2 A:HIS764 4.2 23.3 1.0
CD1 A:PHE762 4.4 30.6 1.0
NE2 A:HIS764 4.6 22.8 1.0
CE2 A:PHE762 4.6 34.5 1.0
CG A:LEU679 4.8 28.6 1.0
C11 A:FEW1001 4.8 30.5 1.0
CD1 A:LEU757 4.8 22.0 1.0
CD2 A:LEU757 4.9 26.8 1.0
C12 A:FEW1001 5.0 31.3 1.0
CB A:ASP784 5.0 30.5 1.0

Fluorine binding site 4 out of 6 in 6gwr

Go back to Fluorine Binding Sites List in 6gwr
Fluorine binding site 4 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2


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 Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:35.0
occ:1.00
 F25 B:FEW1001 0.0 35.0 1.0
C24 B:FEW1001 1.4 33.0 1.0
F26 B:FEW1001 2.2 33.7 1.0
F27 B:FEW1001 2.3 35.5 1.0
C23 B:FEW1001 2.4 35.9 1.0
C22 B:FEW1001 2.7 36.0 1.0
CE1 B:PHE762 3.1 35.0 1.0
CZ B:PHE762 3.4 38.6 1.0
CD1 B:LEU679 3.6 36.5 1.0
C28 B:FEW1001 3.6 32.6 1.0
O B:HOH1145 3.8 38.0 1.0
C13 B:FEW1001 4.1 35.5 1.0
CD1 B:PHE762 4.1 32.9 1.0
CD2 B:HIS764 4.2 29.8 1.0
NE2 B:HIS764 4.5 27.8 1.0
CD1 B:LEU757 4.6 30.5 1.0
CE2 B:PHE762 4.6 39.4 1.0
CB B:ASP784 4.7 35.1 1.0
C11 B:FEW1001 4.7 34.6 1.0
CD2 B:LEU757 4.8 34.9 1.0
CG B:LEU679 4.9 39.6 1.0
C12 B:FEW1001 4.9 34.5 1.0
CG B:HIS764 5.0 28.0 1.0

Fluorine binding site 5 out of 6 in 6gwr

Go back to Fluorine Binding Sites List in 6gwr
Fluorine binding site 5 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2


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 Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:33.7
occ:1.00
 F26 B:FEW1001 0.0 33.7 1.0
C24 B:FEW1001 1.3 33.0 1.0
F25 B:FEW1001 2.2 35.0 1.0
F27 B:FEW1001 2.2 35.5 1.0
C23 B:FEW1001 2.3 35.9 1.0
C28 B:FEW1001 2.7 32.6 1.0
CD1 B:LEU679 3.1 36.5 1.0
C22 B:FEW1001 3.6 36.0 1.0
CG2 B:ILE685 3.8 36.0 1.0
CG2 B:ILE684 3.9 33.4 1.0
O B:ILE782 4.1 32.7 1.0
C11 B:FEW1001 4.1 34.6 1.0
CA B:ALA783 4.3 32.1 1.0
C B:ALA783 4.4 29.9 1.0
CG B:LEU679 4.6 39.6 1.0
C13 B:FEW1001 4.7 35.5 1.0
C B:ILE782 4.7 32.7 1.0
N B:ASP784 4.7 28.3 1.0
O B:ALA783 4.8 30.7 1.0
N B:ALA783 4.8 31.5 1.0
O09 B:FEW1001 4.8 34.2 1.0
C12 B:FEW1001 4.9 34.5 1.0

Fluorine binding site 6 out of 6 in 6gwr

Go back to Fluorine Binding Sites List in 6gwr
Fluorine binding site 6 out of 6 in the Structure of the Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2


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 Kinase Domain of Human DDR1 in Complex with A Potent and Selective Inhibitor of DDR1 and DDR2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1001

b:35.5
occ:1.00
 F27 B:FEW1001 0.0 35.5 1.0
C24 B:FEW1001 1.4 33.0 1.0
F26 B:FEW1001 2.2 33.7 1.0
F25 B:FEW1001 2.3 35.0 1.0
C23 B:FEW1001 2.4 35.9 1.0
O B:ALA783 3.0 30.7 1.0
C B:ALA783 3.0 29.9 1.0
NE2 B:HIS764 3.1 27.8 1.0
C28 B:FEW1001 3.1 32.6 1.0
CB B:ASP784 3.3 35.1 1.0
C22 B:FEW1001 3.3 36.0 1.0
CD2 B:HIS764 3.4 29.8 1.0
N B:ASP784 3.4 28.3 1.0
CA B:ALA783 3.6 32.1 1.0
CA B:ASP784 3.9 33.3 1.0
N B:ALA783 4.1 31.5 1.0
CE1 B:HIS764 4.1 30.2 1.0
O B:HOH1145 4.2 38.0 1.0
CG2 B:ILE782 4.2 28.1 1.0
C11 B:FEW1001 4.4 34.6 1.0
O B:ILE782 4.4 32.7 1.0
C B:ILE782 4.5 32.7 1.0
CG B:ASP784 4.5 35.1 1.0
CG B:HIS764 4.5 28.0 1.0
C13 B:FEW1001 4.5 35.5 1.0
OD2 B:ASP784 4.6 36.1 1.0
O09 B:FEW1001 4.8 34.2 1.0
ND1 B:HIS764 4.8 29.7 1.0
CB B:ALA783 4.9 32.8 1.0
C12 B:FEW1001 4.9 34.5 1.0

Reference:

Z.Wang, Y.Zhang, D.M.Pinkas, A.E.Fox, J.Luo, H.Huang, S.Cui, Q.Xiang, T.Xu, Q.Xun, D.Zhu, Z.Tu, X.Ren, R.A.Brekken, A.N.Bullock, G.Liang, K.Ding, X.Lu. Design, Synthesis, and Biological Evaluation of 3-(Imidazo[1,2- A]Pyrazin-3-Ylethynyl)-4-Isopropyl- N-(3-((4-Methylpiperazin-1-Yl)Methyl)-5-(Trifluoromethyl) Phenyl)Benzamide As A Dual Inhibitor of Discoidin Domain Receptors 1 and 2. J. Med. Chem. V. 61 7977 2018.
ISSN: ISSN 1520-4804
PubMed: 30075624
DOI: 10.1021/ACS.JMEDCHEM.8B01045
Page generated: Tue Jul 15 12:03:39 2025

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