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Fluorine in PDB 5say: DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%

Enzymatic activity of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%

All present enzymatic activity of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%, PDB code: 5say was solved by M.Stihle, H.Richter, J.Benz, R.Hochstrasser, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.52 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.69, 119.59, 61.89, 90, 94.92, 90
R / Rfree (%) 20.2 / 27.7

Other elements in 5say:

The structure of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% also contains other interesting chemical elements:

Iodine (I) 15 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% (pdb code 5say). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%, PDB code: 5say:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5say

Go back to Fluorine Binding Sites List in 5say
Fluorine binding site 1 out of 6 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1009

b:49.8
occ:1.00
 F15 A:1IJ1009 0.0 49.8 1.0
C1 A:1IJ1009 1.3 35.9 1.0
F16 A:1IJ1009 2.1 28.2 1.0
F17 A:1IJ1009 2.1 34.7 1.0
O7 A:1IJ1009 2.2 35.3 1.0
C8 A:1IJ1009 2.9 17.4 1.0
C12 A:1IJ1009 2.9 30.6 1.0
CD1 A:LEU679 3.1 35.4 1.0
CG2 A:ILE685 3.6 19.1 1.0
CG2 A:ILE684 3.7 18.7 1.0
O A:ILE776 3.9 19.8 1.0
C6 A:1IJ1009 4.2 15.4 1.0
C27 A:1IJ1009 4.2 9.2 1.0
CA A:ALA777 4.3 18.1 1.0
CG A:LEU679 4.4 33.0 1.0
C A:ALA777 4.6 23.6 1.0
C A:ILE776 4.6 21.3 1.0
O10 A:1IJ1009 4.7 26.5 1.0
CD2 A:LEU679 4.8 28.8 1.0
O A:ILE685 4.8 36.1 1.0
N A:ALA777 4.8 17.1 1.0
N A:ASP778 4.8 23.3 1.0
C3 A:1IJ1009 4.9 25.5 1.0
CB A:LEU679 4.9 27.1 1.0
N A:ILE685 4.9 18.0 1.0
CB A:ILE685 4.9 23.3 1.0

Fluorine binding site 2 out of 6 in 5say

Go back to Fluorine Binding Sites List in 5say
Fluorine binding site 2 out of 6 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1009

b:28.2
occ:1.00
 F16 A:1IJ1009 0.0 28.2 1.0
C1 A:1IJ1009 1.3 35.9 1.0
F17 A:1IJ1009 2.1 34.7 1.0
F15 A:1IJ1009 2.1 49.8 1.0
O7 A:1IJ1009 2.1 35.3 1.0
C12 A:1IJ1009 3.4 30.6 1.0
CE1 A:PHE756 3.7 22.4 1.0
CD2 A:HIS758 3.8 27.4 1.0
CD1 A:LEU751 3.8 22.9 1.0
C8 A:1IJ1009 4.1 17.4 1.0
CD1 A:LEU679 4.1 35.4 1.0
CZ A:PHE756 4.1 22.1 1.0
CD2 A:LEU751 4.3 18.9 1.0
NE2 A:HIS758 4.4 30.8 1.0
CG2 A:ILE684 4.4 18.7 1.0
C27 A:1IJ1009 4.5 9.2 1.0
CD1 A:PHE756 4.5 19.7 1.0
O A:HOH1149 4.7 29.3 1.0
CG A:LEU751 4.7 23.5 1.0
CD2 A:LEU679 4.7 28.8 1.0
CG A:HIS758 4.8 32.6 1.0
CG2 A:ILE776 4.8 15.1 1.0
O A:ILE776 4.8 19.8 1.0

Fluorine binding site 3 out of 6 in 5say

Go back to Fluorine Binding Sites List in 5say
Fluorine binding site 3 out of 6 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1009

b:34.7
occ:1.00
 F17 A:1IJ1009 0.0 34.7 1.0
C1 A:1IJ1009 1.3 35.9 1.0
F16 A:1IJ1009 2.1 28.2 1.0
F15 A:1IJ1009 2.1 49.8 1.0
O7 A:1IJ1009 2.2 35.3 1.0
C12 A:1IJ1009 2.9 30.6 1.0
C8 A:1IJ1009 3.0 17.4 1.0
C A:ALA777 3.1 23.6 1.0
O A:ALA777 3.3 20.8 1.0
NE2 A:HIS758 3.4 30.8 1.0
CA A:ALA777 3.4 18.1 1.0
CD2 A:HIS758 3.5 27.4 1.0
N A:ASP778 3.5 23.3 1.0
CB A:ASP778 3.7 24.3 1.0
N A:ALA777 3.9 17.1 1.0
O A:ILE776 4.0 19.8 1.0
CG2 A:ILE776 4.2 15.1 1.0
C27 A:1IJ1009 4.2 9.2 1.0
C A:ILE776 4.2 21.3 1.0
CA A:ASP778 4.2 27.0 1.0
C6 A:1IJ1009 4.2 15.4 1.0
O A:HOH1149 4.4 29.3 1.0
CE1 A:HIS758 4.5 30.6 1.0
CG A:HIS758 4.7 32.6 1.0
O10 A:1IJ1009 4.7 26.5 1.0
CB A:ALA777 4.8 27.1 1.0
CG2 A:ILE685 4.8 19.1 1.0

Fluorine binding site 4 out of 6 in 5say

Go back to Fluorine Binding Sites List in 5say
Fluorine binding site 4 out of 6 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1008

b:51.0
occ:1.00
 F15 B:1IJ1008 0.0 51.0 1.0
C1 B:1IJ1008 1.3 37.2 1.0
F16 B:1IJ1008 2.1 26.3 1.0
F17 B:1IJ1008 2.1 32.4 1.0
O7 B:1IJ1008 2.2 25.9 1.0
C8 B:1IJ1008 2.9 28.3 1.0
C12 B:1IJ1008 2.9 25.2 1.0
CD1 B:LEU679 3.3 53.8 1.0
CG2 B:ILE685 3.6 23.4 1.0
CG2 B:ILE684 3.6 17.0 1.0
O B:ILE776 3.9 27.3 1.0
CA B:ALA777 4.1 26.4 1.0
C6 B:1IJ1008 4.2 23.9 1.0
C27 B:1IJ1008 4.2 22.2 1.0
C B:ALA777 4.5 27.0 1.0
O10 B:1IJ1008 4.6 26.7 1.0
C B:ILE776 4.6 24.7 1.0
CG B:LEU679 4.7 35.4 1.0
N B:ALA777 4.7 25.3 1.0
N B:ILE685 4.8 17.5 1.0
O B:ILE685 4.8 27.4 1.0
N B:ASP778 4.8 36.1 1.0
C3 B:1IJ1008 4.8 28.1 1.0
CB B:ILE685 4.9 22.8 1.0
CB B:LEU679 5.0 25.4 1.0

Fluorine binding site 5 out of 6 in 5say

Go back to Fluorine Binding Sites List in 5say
Fluorine binding site 5 out of 6 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1008

b:26.3
occ:1.00
 F16 B:1IJ1008 0.0 26.3 1.0
C1 B:1IJ1008 1.3 37.2 1.0
F17 B:1IJ1008 2.1 32.4 1.0
F15 B:1IJ1008 2.1 51.0 1.0
O7 B:1IJ1008 2.2 25.9 1.0
C12 B:1IJ1008 3.6 25.2 1.0
CD1 B:LEU679 3.7 53.8 1.0
CD1 B:LEU751 3.8 19.4 1.0
CE2 B:PHE756 3.8 15.9 1.0
CD2 B:LEU751 4.0 27.4 1.0
CG2 B:ILE684 4.1 17.0 1.0
CD2 B:HIS758 4.2 24.7 1.0
C8 B:1IJ1008 4.2 28.3 1.0
CD2 B:PHE756 4.4 16.3 1.0
CG B:LEU751 4.5 19.3 1.0
CZ B:PHE756 4.6 23.8 1.0
C27 B:1IJ1008 4.6 22.2 1.0
NE2 B:HIS758 4.7 20.7 1.0
CG B:LEU679 4.8 35.4 1.0
CD1 B:ILE684 4.8 16.3 1.0
CD2 B:LEU679 4.9 19.3 1.0
O B:ILE776 4.9 27.3 1.0
CG2 B:ILE776 4.9 14.5 1.0

Fluorine binding site 6 out of 6 in 5say

Go back to Fluorine Binding Sites List in 5say
Fluorine binding site 6 out of 6 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1008

b:32.4
occ:1.00
 F17 B:1IJ1008 0.0 32.4 1.0
C1 B:1IJ1008 1.3 37.2 1.0
F16 B:1IJ1008 2.1 26.3 1.0
F15 B:1IJ1008 2.1 51.0 1.0
O7 B:1IJ1008 2.2 25.9 1.0
C12 B:1IJ1008 3.0 25.2 1.0
C8 B:1IJ1008 3.0 28.3 1.0
C B:ALA777 3.3 27.0 1.0
O B:ALA777 3.4 30.7 1.0
NE2 B:HIS758 3.4 20.7 1.0
CA B:ALA777 3.5 26.4 1.0
CD2 B:HIS758 3.5 24.7 1.0
N B:ASP778 3.7 36.1 1.0
CB B:ASP778 4.0 34.9 1.0
N B:ALA777 4.0 25.3 1.0
C27 B:1IJ1008 4.2 22.2 1.0
O B:ILE776 4.2 27.3 1.0
CG2 B:ILE776 4.3 14.5 1.0
C B:ILE776 4.3 24.7 1.0
C6 B:1IJ1008 4.4 23.9 1.0
CA B:ASP778 4.4 25.0 1.0
CE1 B:HIS758 4.5 24.4 1.0
CG B:HIS758 4.7 24.3 1.0
O10 B:1IJ1008 4.8 26.7 1.0
CB B:ALA777 4.9 34.2 1.0

Reference:

H.Richter, M.Prunotto, B.Kuhn, M.G.Rudolph. Crystal Structure of A DDR1 Complex To Be Published.
Page generated: Thu Aug 1 14:10:52 2024

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