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Iodine in PDB 5sav: DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%

Enzymatic activity of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%

All present enzymatic activity of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%, PDB code: 5sav 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) 41.15 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44, 62.56, 109.28, 90, 90, 90
R / Rfree (%) 19.3 / 23.5

Other elements in 5sav:

The structure of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5% also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5% (pdb code 5sav). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%, PDB code: 5sav:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 5sav

Go back to Iodine Binding Sites List in 5sav
Iodine binding site 1 out of 3 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%


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-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:19.9
occ:1.00
 O A:HOH1362 3.4 47.0 1.0
O A:HOH1266 3.4 17.3 1.0
CA A:PHE839 3.8 13.7 1.0
CB A:GLN841 3.8 25.4 1.0
N A:GLN841 3.8 15.7 1.0
C A:PHE839 3.9 14.3 1.0
N A:GLY840 4.1 12.4 1.0
CG A:LEU842 4.3 22.1 1.0
CG A:GLN841 4.3 21.6 1.0
CA A:GLN841 4.3 18.6 1.0
O A:PHE839 4.4 14.6 1.0
O A:HOH1318 4.6 42.1 1.0
N A:LEU842 4.6 16.4 1.0
CD1 A:LEU842 4.7 20.9 1.0
N A:PHE839 4.7 16.3 1.0
C A:GLN841 4.7 24.8 1.0
CD1 A:PHE839 4.7 21.0 1.0
CB A:PHE839 4.8 16.9 1.0
O A:HOH1235 4.8 23.1 1.0
O A:HOH1342 4.9 37.1 1.0
C A:GLY840 4.9 21.4 1.0

Iodine binding site 2 out of 3 in 5sav

Go back to Iodine Binding Sites List in 5sav
Iodine binding site 2 out of 3 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:61.6
occ:1.00
 N A:LEU718 3.6 25.3 1.0
NE2 A:GLN717 3.7 57.7 1.0
CA A:GLN717 4.0 24.3 1.0
NH2 A:ARG835 4.2 31.0 1.0
CG A:GLN717 4.3 39.2 1.0
CB A:GLN717 4.3 27.5 1.0
C A:GLN717 4.3 29.5 1.0
CB A:LEU718 4.4 20.4 1.0
CD A:GLN717 4.4 54.2 1.0
CD2 A:LEU833 4.5 28.8 1.0
CZ A:ARG835 4.6 27.9 1.0
CA A:LEU718 4.6 29.1 1.0
CD1 A:LEU833 4.7 33.1 1.0
O A:HOH1174 4.7 36.5 1.0
NE A:ARG835 4.8 31.5 1.0
O A:HIS716 4.8 27.5 1.0

Iodine binding site 3 out of 3 in 5sav

Go back to Iodine Binding Sites List in 5sav
Iodine binding site 3 out of 3 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 1.760A, P212121, Rfree=23.5% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:75.7
occ:1.00
 NE2 A:HIS896 3.4 25.3 1.0
O A:HOH1289 3.5 49.6 1.0
O A:HOH1246 3.7 26.1 1.0
O A:HOH1127 3.8 36.7 1.0
CB A:ALA742 4.0 18.6 1.0
CD2 A:HIS896 4.1 20.9 1.0
C A:ALA742 4.1 16.7 1.0
O A:ALA742 4.2 16.9 1.0
N A:GLN743 4.2 17.1 1.0
CG A:GLN743 4.2 17.4 1.0
CA A:GLN743 4.3 15.7 1.0
CE1 A:HIS896 4.5 27.1 1.0
CB A:SER746 4.6 21.7 1.0
CA A:ALA742 4.7 13.8 1.0
CB A:GLN743 4.9 16.0 1.0
CB A:ALA900 4.9 22.9 1.0
ND1 A:HIS739 4.9 26.7 1.0
OG A:SER746 4.9 17.3 1.0
CE1 A:HIS739 4.9 25.3 1.0

Reference:

H.Richter, M.Prunotto, B.Kuhn, M.G.Rudolph. Crystal Structure of A DDR1 Complex To Be Published.
Page generated: Fri Aug 8 20:19:23 2025

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