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Fluorine in PDB 5sau: DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%

Enzymatic activity of DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%

All present enzymatic activity of DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%, PDB code: 5sau 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) 48.05 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.514, 74.156, 75.105, 90, 90, 90
R / Rfree (%) 19.9 / 23.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1% (pdb code 5sau). 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, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%, PDB code: 5sau:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5sau

Go back to Fluorine Binding Sites List in 5sau
Fluorine binding site 1 out of 3 in the DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:34.7
occ:1.00
 F18 A:1IF1000 0.0 34.7 1.0
C17 A:1IF1000 1.3 33.6 1.0
F20 A:1IF1000 2.1 35.2 1.0
F19 A:1IF1000 2.1 35.0 1.0
C15 A:1IF1000 2.4 28.0 1.0
C14 A:1IF1000 2.8 32.8 1.0
CD1 A:LEU679 3.5 40.4 1.0
CE2 A:PHE756 3.6 30.3 1.0
C16 A:1IF1000 3.7 30.7 1.0
CZ A:PHE756 3.9 35.4 1.0
O A:HOH1132 3.9 33.2 1.0
CD2 A:HIS758 4.1 28.6 1.0
C13 A:1IF1000 4.2 34.4 1.0
CD2 A:PHE756 4.6 31.6 1.0
NE2 A:HIS758 4.6 30.1 1.0
CG A:LEU679 4.8 37.5 1.0
CD2 A:LEU679 4.8 36.3 1.0
C11 A:1IF1000 4.8 31.5 1.0
CB A:ASP778 4.9 32.3 1.0
CD1 A:LEU751 5.0 32.7 1.0
CG2 A:ILE684 5.0 29.1 1.0

Fluorine binding site 2 out of 3 in 5sau

Go back to Fluorine Binding Sites List in 5sau
Fluorine binding site 2 out of 3 in the DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:35.0
occ:1.00
 F19 A:1IF1000 0.0 35.0 1.0
C17 A:1IF1000 1.4 33.6 1.0
F18 A:1IF1000 2.1 34.7 1.0
F20 A:1IF1000 2.1 35.2 1.0
C15 A:1IF1000 2.4 28.0 1.0
C16 A:1IF1000 3.1 30.7 1.0
O A:ALA777 3.2 26.9 1.0
C A:ALA777 3.2 25.8 1.0
NE2 A:HIS758 3.2 30.1 1.0
C14 A:1IF1000 3.3 32.8 1.0
CD2 A:HIS758 3.4 28.6 1.0
CB A:ASP778 3.6 32.3 1.0
CA A:ALA777 3.7 28.4 1.0
N A:ASP778 3.7 28.1 1.0
N A:ALA777 4.1 26.1 1.0
O A:HOH1132 4.1 33.2 1.0
CA A:ASP778 4.2 29.9 1.0
O A:ILE776 4.2 29.2 1.0
CG2 A:ILE776 4.3 31.6 1.0
C A:ILE776 4.4 29.7 1.0
C11 A:1IF1000 4.4 31.5 1.0
CE1 A:HIS758 4.4 28.6 1.0
C13 A:1IF1000 4.5 34.4 1.0
CG A:HIS758 4.6 26.2 1.0
CG A:ASP778 4.7 33.7 1.0
OD2 A:ASP778 4.9 33.6 1.0
O9 A:1IF1000 4.9 31.1 1.0
C12 A:1IF1000 5.0 34.8 1.0

Fluorine binding site 3 out of 3 in 5sau

Go back to Fluorine Binding Sites List in 5sau
Fluorine binding site 3 out of 3 in the DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1%


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of DDR1, 3-[2-(6-Aminopyridin-3-Yl)Ethynyl]-N-[3-(Trifluoromethyl) Phenyl]Benzamide, 1.800A, P212121, Rfree=23.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1000

b:35.2
occ:1.00
 F20 A:1IF1000 0.0 35.2 1.0
C17 A:1IF1000 1.3 33.6 1.0
F18 A:1IF1000 2.1 34.7 1.0
F19 A:1IF1000 2.1 35.0 1.0
C15 A:1IF1000 2.4 28.0 1.0
C16 A:1IF1000 2.8 30.7 1.0
CD1 A:LEU679 3.2 40.4 1.0
CG2 A:ILE685 3.5 32.1 1.0
C14 A:1IF1000 3.6 32.8 1.0
CG2 A:ILE684 3.8 29.1 1.0
O A:ILE776 3.9 29.2 1.0
C11 A:1IF1000 4.2 31.5 1.0
CA A:ALA777 4.3 28.4 1.0
C A:ALA777 4.5 25.8 1.0
C A:ILE776 4.6 29.7 1.0
CG A:LEU679 4.7 37.5 1.0
C13 A:1IF1000 4.7 34.4 1.0
N A:ALA777 4.8 26.1 1.0
O9 A:1IF1000 4.8 31.1 1.0
N A:ASP778 4.8 28.1 1.0
O A:ALA777 4.9 26.9 1.0
N A:ILE685 4.9 30.2 1.0
CB A:ILE685 4.9 33.7 1.0
C12 A:1IF1000 5.0 34.8 1.0

Reference:

H.Richter, M.Prunotto, B.Kuhn, M.G.Rudolph. Crystal Structure of A DDR1 Complex To Be Published.
Page generated: Tue Jul 15 07:06:33 2025

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