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Iodine 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
Fluorine (F) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total only one binding site of Iodine was determined in the DDR1, N-[[2-(2-Pyridin-3-Yloxyethyl)Cyclohexyl]Methyl]-3- (Trifluoromethoxy)Benzamide, 1.970A, P212121, Rfree=25.6%, PDB code: 5sb0:

Iodine binding site 1 out of 1 in 5sb0

Go back to Iodine Binding Sites List in 5sb0
Iodine binding site 1 out of 1 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 Iodine with other atoms in the I 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:I1001

b:48.0
occ:1.00
 O A:HOH1181 3.5 29.0 1.0
CA A:PHE839 3.9 33.9 1.0
N A:GLN841 4.0 33.5 1.0
C A:PHE839 4.0 35.3 1.0
N A:GLY840 4.1 31.9 1.0
CB A:GLN841 4.2 37.3 1.0
CG A:LEU842 4.3 38.0 1.0
CA A:GLN841 4.5 35.2 1.0
O A:PHE839 4.6 35.1 1.0
CG A:GLN841 4.6 39.1 1.0
N A:LEU842 4.7 32.4 1.0
N A:PHE839 4.7 30.8 1.0
CD1 A:PHE839 4.8 35.8 1.0
O A:HOH1177 4.8 34.3 1.0
CB A:PHE839 4.8 34.0 1.0
CD2 A:LEU842 4.8 34.9 1.0
CD1 A:LEU842 4.9 33.6 1.0
C A:GLN841 4.9 38.8 1.0
O A:HOH1148 4.9 39.7 1.0
C A:GLY840 5.0 35.4 1.0

Reference:

H.Richter, M.Prunotto, B.Kuhn, M.G.Rudolph. Crystal Structure of A DDR1 Complex To Be Published.
Page generated: Sun Aug 11 21:51:06 2024

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