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Fluorine in PDB 5sb0: DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%

Enzymatic activity of DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%

All present enzymatic activity of DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%, PDB code: 5sb0 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) 48.23 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.056, 76.661, 77.783, 90, 90, 90
R / Rfree (%) 20.8 / 25.6

Other elements in 5sb0:

The structure of DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6% also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Iodine (I) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6% (pdb code 5sb0). 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, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%, PDB code: 5sb0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5sb0

Go back to Fluorine Binding Sites List in 5sb0
Fluorine binding site 1 out of 3 in the DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%


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-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:42.9
occ:1.00
 F22 A:1IZ1002 0.0 42.9 1.0
C21 A:1IZ1002 1.3 41.2 1.0
F24 A:1IZ1002 2.1 48.9 1.0
F23 A:1IZ1002 2.2 39.9 1.0
O20 A:1IZ1002 2.2 38.8 1.0
C16 A:1IZ1002 2.8 40.0 1.0
C15 A:1IZ1002 2.9 34.5 1.0
C A:ALA777 3.1 33.3 1.0
CA A:ALA777 3.2 36.0 1.0
O A:ALA777 3.3 33.2 1.0
N A:ASP778 3.5 30.5 1.0
NE2 A:HIS758 3.7 34.8 1.0
O A:ILE776 3.7 31.4 1.0
N A:ALA777 3.8 34.7 1.0
CD2 A:HIS758 3.9 37.5 1.0
CB A:ASP778 3.9 36.6 1.0
C A:ILE776 4.0 33.1 1.0
C17 A:1IZ1002 4.1 41.5 1.0
C7 A:1IZ1002 4.1 35.9 1.0
CG2 A:ILE685 4.2 32.5 1.0
CG2 A:ILE776 4.3 35.9 1.0
CA A:ASP778 4.3 33.6 1.0
O6 A:1IZ1002 4.5 34.6 1.0
CB A:ALA777 4.6 33.6 1.0
CG2 A:ILE684 4.8 36.1 1.0
C5 A:1IZ1002 4.8 36.2 1.0
CE1 A:HIS758 4.8 36.6 1.0
CD1 A:LEU679 4.9 43.2 1.0
CB A:ILE776 5.0 35.1 1.0

Fluorine binding site 2 out of 3 in 5sb0

Go back to Fluorine Binding Sites List in 5sb0
Fluorine binding site 2 out of 3 in the DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%


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-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:39.9
occ:1.00
 F23 A:1IZ1002 0.0 39.9 1.0
C21 A:1IZ1002 1.3 41.2 1.0
F22 A:1IZ1002 2.2 42.9 1.0
F24 A:1IZ1002 2.2 48.9 1.0
O20 A:1IZ1002 2.2 38.8 1.0
C16 A:1IZ1002 3.5 40.0 1.0
CD1 A:LEU679 3.7 43.2 1.0
CD2 A:HIS758 3.8 37.5 1.0
CD1 A:LEU751 3.9 34.8 1.0
CG2 A:ILE684 4.0 36.1 1.0
CE1 A:PHE756 4.0 36.3 1.0
C15 A:1IZ1002 4.2 34.5 1.0
CD2 A:LEU751 4.3 35.4 1.0
NE2 A:HIS758 4.4 34.8 1.0
C17 A:1IZ1002 4.5 41.5 1.0
CZ A:PHE756 4.6 35.1 1.0
CD1 A:PHE756 4.7 34.8 1.0
O A:ILE776 4.7 31.4 1.0
CG A:LEU751 4.7 35.3 1.0
CG2 A:ILE776 4.7 35.9 1.0
CD1 A:ILE684 4.8 32.5 1.0
CG A:HIS758 4.9 36.1 1.0
CG A:LEU679 4.9 41.0 1.0

Fluorine binding site 3 out of 3 in 5sb0

Go back to Fluorine Binding Sites List in 5sb0
Fluorine binding site 3 out of 3 in the DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%


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-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1002

b:48.9
occ:1.00
 F24 A:1IZ1002 0.0 48.9 1.0
C21 A:1IZ1002 1.3 41.2 1.0
F22 A:1IZ1002 2.1 42.9 1.0
F23 A:1IZ1002 2.2 39.9 1.0
O20 A:1IZ1002 2.2 38.8 1.0
C16 A:1IZ1002 2.7 40.0 1.0
O A:HOH1133 3.1 41.8 1.0
CD2 A:HIS758 3.2 37.5 1.0
NE2 A:HIS758 3.4 34.8 1.0
C17 A:1IZ1002 3.4 41.5 1.0
C15 A:1IZ1002 3.5 34.5 1.0
CB A:ASP778 3.7 36.6 1.0
CE1 A:PHE756 3.9 36.3 1.0
CG A:HIS758 4.0 36.1 1.0
CE1 A:HIS758 4.2 36.6 1.0
O A:ALA777 4.3 33.2 1.0
CZ A:PHE756 4.3 35.1 1.0
OD2 A:ASP778 4.4 40.9 1.0
C A:ALA777 4.4 33.3 1.0
C18 A:1IZ1002 4.5 41.4 1.0
ND1 A:HIS758 4.5 36.4 1.0
CG A:ASP778 4.6 42.2 1.0
N A:ASP778 4.6 30.5 1.0
C7 A:1IZ1002 4.6 35.9 1.0
CA A:ASP778 4.8 33.6 1.0
CB A:HIS758 4.9 35.2 1.0
CA A:HIS758 4.9 34.2 1.0
CD1 A:LEU679 4.9 43.2 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 14:12:32 2024

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