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Fluorine in PDB 5sax: DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form

Enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form

All present enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form, PDB code: 5sax 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) 40.07 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.25, 73.76, 74.31, 90, 90, 90
R / Rfree (%) 20.9 / 25.4

Other elements in 5sax:

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form also contains other interesting chemical elements:

Iodine (I) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form (pdb code 5sax). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form, PDB code: 5sax:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5sax

Go back to Fluorine Binding Sites List in 5sax
Fluorine binding site 1 out of 3 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1009

b:40.5
occ:1.00
 F19 A:1IM1009 0.0 40.5 1.0
C18 A:1IM1009 1.3 35.2 1.0
F21 A:1IM1009 2.1 42.1 1.0
F20 A:1IM1009 2.1 33.3 1.0
C16 A:1IM1009 2.4 37.5 1.0
C17 A:1IM1009 3.0 34.7 1.0
CG2 A:ILE685 3.3 32.7 1.0
C15 A:1IM1009 3.5 32.6 1.0
CD1 A:LEU679 3.5 42.5 1.0
CG2 A:ILE684 3.5 31.3 1.0
O A:ILE776 4.0 33.7 1.0
CA A:ALA777 4.3 34.3 1.0
C12 A:1IM1009 4.3 35.2 1.0
O A:ILE685 4.6 35.3 1.0
N A:ILE685 4.6 29.8 1.0
CB A:ILE685 4.6 35.2 1.0
C14 A:1IM1009 4.6 38.2 1.0
C A:ALA777 4.7 33.6 1.0
C A:ILE776 4.7 27.3 1.0
CG A:LEU679 4.8 35.4 1.0
N A:ALA777 4.9 28.6 1.0
CB A:ILE684 4.9 32.9 1.0
C13 A:1IM1009 5.0 37.2 1.0

Fluorine binding site 2 out of 3 in 5sax

Go back to Fluorine Binding Sites List in 5sax
Fluorine binding site 2 out of 3 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1009

b:33.3
occ:1.00
 F20 A:1IM1009 0.0 33.3 1.0
C18 A:1IM1009 1.3 35.2 1.0
F21 A:1IM1009 2.1 42.1 1.0
F19 A:1IM1009 2.1 40.5 1.0
C16 A:1IM1009 2.3 37.5 1.0
C15 A:1IM1009 2.7 32.6 1.0
CD1 A:LEU679 3.4 42.5 1.0
C17 A:1IM1009 3.6 34.7 1.0
CE1 A:PHE756 3.9 30.5 1.0
CD2 A:HIS758 4.0 34.2 1.0
C14 A:1IM1009 4.1 38.2 1.0
O A:HOH1194 4.2 39.3 1.0
CZ A:PHE756 4.2 37.0 1.0
NE2 A:HIS758 4.5 29.6 1.0
CD1 A:LEU751 4.6 30.8 1.0
CG2 A:ILE684 4.6 31.3 1.0
CD1 A:PHE756 4.7 32.9 1.0
C12 A:1IM1009 4.8 35.2 1.0
CG A:LEU679 4.9 35.4 1.0
CD2 A:LEU751 4.9 34.3 1.0
C13 A:1IM1009 4.9 37.2 1.0

Fluorine binding site 3 out of 3 in 5sax

Go back to Fluorine Binding Sites List in 5sax
Fluorine binding site 3 out of 3 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1009

b:42.1
occ:1.00
 F21 A:1IM1009 0.0 42.1 1.0
C18 A:1IM1009 1.4 35.2 1.0
F20 A:1IM1009 2.1 33.3 1.0
F19 A:1IM1009 2.1 40.5 1.0
C16 A:1IM1009 2.4 37.5 1.0
C17 A:1IM1009 3.0 34.7 1.0
C A:ALA777 3.1 33.6 1.0
O A:ALA777 3.2 26.3 1.0
CA A:ALA777 3.3 34.3 1.0
C15 A:1IM1009 3.5 32.6 1.0
NE2 A:HIS758 3.5 29.6 1.0
N A:ASP778 3.6 30.9 1.0
CD2 A:HIS758 3.7 34.2 1.0
N A:ALA777 3.8 28.6 1.0
O A:ILE776 3.8 33.7 1.0
CB A:ASP778 4.0 32.9 1.0
C A:ILE776 4.0 27.3 1.0
CG2 A:ILE776 4.0 30.2 1.0
C12 A:1IM1009 4.3 35.2 1.0
CA A:ASP778 4.4 34.4 1.0
CG2 A:ILE685 4.4 32.7 1.0
CB A:ALA777 4.6 31.2 1.0
C14 A:1IM1009 4.6 38.2 1.0
CE1 A:HIS758 4.7 33.6 1.0
O A:HOH1194 4.8 39.3 1.0
O11 A:1IM1009 4.8 30.0 1.0
CB A:ILE776 4.9 29.8 1.0
CG2 A:ILE684 4.9 31.3 1.0
CG A:HIS758 5.0 31.9 1.0
C13 A:1IM1009 5.0 37.2 1.0

Reference:

H.Richter, M.Prunotto, B.Kuhn, M.G.Rudolph. Crystal Structure of A DDR1 Complex To Be Published.
Page generated: Tue Apr 4 23:41:25 2023

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