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Fluorine in PDB 5saw: DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%

Enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%

All present enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%, PDB code: 5saw 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) 44.07 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.63, 61.64, 116.14, 90, 90, 90
R / Rfree (%) 19.9 / 22.6

Other elements in 5saw:

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% also contains other interesting chemical elements:

Iodine (I) 10 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, 1.601A, P212121, Rfree=22.6% (pdb code 5saw). 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, 1.601A, P212121, Rfree=22.6%, PDB code: 5saw:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5saw

Go back to Fluorine Binding Sites List in 5saw
Fluorine binding site 1 out of 3 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


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, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:17.3
occ:1.00
 F19 A:1IM1001 0.0 17.3 1.0
C18 A:1IM1001 1.3 17.8 1.0
F21 A:1IM1001 2.1 16.9 1.0
F20 A:1IM1001 2.1 17.6 1.0
C16 A:1IM1001 2.4 15.5 1.0
C17 A:1IM1001 2.9 13.2 1.0
CD1 A:LEU679 3.2 16.6 1.0
CG2 A:ILE685 3.3 13.7 1.0
CG2 A:ILE684 3.5 12.9 1.0
O A:ILE776 3.5 13.7 1.0
C15 A:1IM1001 3.6 16.4 1.0
CA A:ALA777 3.9 12.2 1.0
C A:ILE776 4.2 11.9 1.0
C A:ALA777 4.3 12.5 1.0
C12 A:1IM1001 4.3 14.9 1.0
N A:ALA777 4.4 13.1 1.0
CG A:LEU679 4.5 19.6 1.0
N A:ILE685 4.6 11.4 1.0
CB A:ILE685 4.6 14.8 1.0
O A:ALA777 4.7 11.5 1.0
N A:ASP778 4.7 10.8 1.0
CD2 A:LEU679 4.7 21.1 1.0
C14 A:1IM1001 4.7 16.3 1.0
O11 A:1IM1001 4.8 12.3 1.0
O A:ILE685 4.8 13.3 1.0
CB A:ILE684 4.9 13.7 1.0

Fluorine binding site 2 out of 3 in 5saw

Go back to Fluorine Binding Sites List in 5saw
Fluorine binding site 2 out of 3 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


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, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:17.6
occ:1.00
 F20 A:1IM1001 0.0 17.6 1.0
C18 A:1IM1001 1.3 17.8 1.0
F21 A:1IM1001 2.1 16.9 1.0
F19 A:1IM1001 2.1 17.3 1.0
C16 A:1IM1001 2.4 15.5 1.0
C15 A:1IM1001 2.7 16.4 1.0
C17 A:1IM1001 3.6 13.2 1.0
CE1 A:PHE756 3.7 14.9 1.0
CD1 A:LEU679 3.8 16.6 1.0
C14 A:1IM1001 4.1 16.3 1.0
CZ A:PHE756 4.1 18.4 1.0
CD2 A:HIS758 4.1 12.1 1.0
CD2 A:LEU679 4.2 21.1 1.0
O A:HOH1199 4.4 16.1 1.0
CD1 A:LEU751 4.4 12.5 1.0
CG2 A:ILE684 4.5 12.9 1.0
NE2 A:HIS758 4.6 13.7 1.0
CG A:LEU679 4.6 19.6 1.0
CD1 A:PHE756 4.6 14.8 1.0
CD2 A:LEU751 4.7 14.8 1.0
C12 A:1IM1001 4.8 14.9 1.0
C13 A:1IM1001 4.9 16.4 1.0

Fluorine binding site 3 out of 3 in 5saw

Go back to Fluorine Binding Sites List in 5saw
Fluorine binding site 3 out of 3 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


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, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1001

b:16.9
occ:1.00
 F21 A:1IM1001 0.0 16.9 1.0
C18 A:1IM1001 1.3 17.8 1.0
F20 A:1IM1001 2.1 17.6 1.0
F19 A:1IM1001 2.1 17.3 1.0
C16 A:1IM1001 2.3 15.5 1.0
C17 A:1IM1001 3.0 13.2 1.0
O A:ALA777 3.1 11.5 1.0
C A:ALA777 3.2 12.5 1.0
NE2 A:HIS758 3.2 13.7 1.0
C15 A:1IM1001 3.3 16.4 1.0
CD2 A:HIS758 3.3 12.1 1.0
CA A:ALA777 3.5 12.2 1.0
CB A:ASP778 3.7 12.6 1.0
N A:ASP778 3.7 10.8 1.0
N A:ALA777 4.0 13.1 1.0
CG2 A:ILE776 4.1 11.3 1.0
O A:ILE776 4.2 13.7 1.0
CA A:ASP778 4.2 11.3 1.0
C A:ILE776 4.3 11.9 1.0
C12 A:1IM1001 4.3 14.9 1.0
O A:HOH1199 4.4 16.1 1.0
CE1 A:HIS758 4.4 13.7 1.0
C14 A:1IM1001 4.4 16.3 1.0
CG A:HIS758 4.5 12.5 1.0
CG2 A:ILE685 4.9 13.7 1.0
C13 A:1IM1001 4.9 16.4 1.0
CG A:ASP778 4.9 15.7 1.0
CB A:ALA777 4.9 13.3 1.0
O11 A:1IM1001 5.0 12.3 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 14:10:23 2024

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