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Iodine in PDB 5say: DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%

Enzymatic activity of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%

All present enzymatic activity of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%, PDB code: 5say 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) 45.52 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.69, 119.59, 61.89, 90, 94.92, 90
R / Rfree (%) 20.2 / 27.7

Other elements in 5say:

The structure of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% (pdb code 5say). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%, PDB code: 5say:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 1 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


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, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:35.6
occ:1.00
 I A:IOD1005 3.7 119.2 1.0
CA A:PHE839 3.8 24.5 1.0
C A:PHE839 3.8 23.1 1.0
N A:GLN841 3.9 35.0 1.0
CB A:GLN841 4.0 24.2 1.0
O A:PHE839 4.1 26.3 1.0
N A:GLY840 4.2 24.3 1.0
CG A:LEU842 4.3 24.9 1.0
CA A:GLN841 4.4 23.5 1.0
N A:LEU842 4.5 28.4 1.0
CG A:GLN841 4.6 28.9 1.0
CD2 A:LEU842 4.6 22.6 1.0
CB A:PHE839 4.8 16.9 1.0
C A:GLN841 4.8 23.7 1.0
N A:PHE839 4.8 29.0 1.0
CD1 A:PHE839 4.9 19.0 1.0
C A:GLY840 4.9 21.4 1.0

Iodine binding site 2 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 2 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


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, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:68.6
occ:1.00
 NH1 A:ARG880 3.4 53.4 1.0
OE1 A:GLN894 3.5 50.6 1.0
CD1 A:LEU877 3.5 46.2 1.0
CG A:GLN894 3.6 43.8 1.0
CD A:GLN894 4.0 51.3 1.0
CB A:PRO890 4.0 33.5 1.0
O A:GLN894 4.1 34.9 1.0
CG A:PRO890 4.1 23.9 1.0
CG A:LEU877 4.2 38.5 1.0
CD2 A:LEU895 4.4 35.4 1.0
CZ A:ARG880 4.4 62.3 1.0
C A:GLN894 4.4 31.8 1.0
CB A:PHE898 4.4 27.7 1.0
CD2 A:PHE898 4.5 40.2 1.0
CD A:ARG880 4.7 20.2 1.0
CG A:PHE898 4.7 43.2 1.0
N A:LEU895 4.7 35.9 1.0
CA A:LEU895 4.7 25.0 1.0
CB A:GLN894 4.8 39.1 1.0
NE A:ARG880 4.9 65.8 1.0
CB A:LEU877 5.0 39.3 1.0

Iodine binding site 3 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 3 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


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, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:90.3
occ:1.00
 NE A:ARG783 3.1 26.7 1.0
NH2 A:ARG783 3.2 20.2 1.0
O A:GLY780 3.3 47.5 1.0
CZ A:ARG783 3.6 24.5 1.0
CB A:ARG783 3.8 46.4 1.0
OH A:TYR790 3.9 34.6 1.0
N A:ARG783 4.2 60.4 1.0
CE2 A:TYR790 4.2 19.2 1.0
CD2 A:TYR786 4.2 28.1 1.0
CG A:ARG783 4.2 40.6 1.0
CD A:ARG783 4.3 31.9 1.0
C A:GLY780 4.3 48.7 1.0
CB A:TYR786 4.3 20.8 1.0
CA A:MET781 4.3 38.3 1.0
CB A:PHE779 4.4 28.1 1.0
CD A:ARG764 4.5 16.6 1.0
CZ A:TYR790 4.5 34.8 1.0
O A:HOH1111 4.5 32.5 1.0
CA A:ARG783 4.5 52.7 1.0
O A:ARG783 4.6 37.6 1.0
N A:SER782 4.6 72.3 1.0
C A:MET781 4.6 61.8 1.0
CG A:TYR786 4.7 30.2 1.0
N A:MET781 4.8 48.0 1.0
NE A:ARG764 4.8 24.2 1.0
OD1 A:ASN765 4.8 28.5 1.0
NH1 A:ARG783 4.9 32.5 1.0

Iodine binding site 4 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 4 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:104.0
occ:1.00
 O A:HOH1147 3.3 22.1 1.0
CA A:GLY873 4.0 31.0 1.0
N A:LEU874 4.0 30.4 1.0
CB A:PRO871 4.3 23.8 1.0
C A:GLY873 4.3 30.1 1.0
N A:GLY873 4.4 23.8 1.0
OH A:TYR734 4.8 43.4 1.0
CA A:LEU874 4.9 37.3 1.0
CZ A:PHE898 4.9 38.0 1.0
CG A:PRO871 4.9 21.7 1.0

Iodine binding site 5 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 5 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:119.2
occ:1.00
 CD2 A:LEU864 3.7 31.0 1.0
I A:IOD1001 3.7 35.6 1.0
CZ2 A:TRP828 3.9 16.7 1.0
N A:PHE839 4.1 29.0 1.0
N A:SER865 4.2 16.6 1.0
O A:HOH1150 4.2 26.6 1.0
O A:HOH1203 4.2 48.5 1.0
CA A:PHE839 4.3 24.5 1.0
CH2 A:TRP828 4.4 16.7 1.0
CA A:LEU864 4.5 20.8 1.0
OG A:SER865 4.6 41.1 1.0
CE2 A:TRP828 4.7 19.3 1.0
CB A:SER865 4.8 26.1 1.0
CB A:LEU864 4.8 21.3 1.0
N A:GLY840 4.8 24.3 1.0
CG A:LEU864 4.8 25.6 1.0
C A:LEU864 4.9 17.4 1.0
NE1 A:TRP828 5.0 22.6 1.0

Iodine binding site 6 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 6 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:102.6
occ:1.00
 NE2 A:HIS896 3.5 34.4 1.0
CB A:ALA742 4.2 18.1 1.0
CG A:GLN743 4.2 19.1 1.0
N A:GLN743 4.3 20.1 1.0
CD2 A:HIS896 4.3 31.9 1.0
C A:ALA742 4.3 24.5 1.0
CA A:GLN743 4.3 24.0 1.0
O A:ALA742 4.5 20.0 1.0
CE1 A:HIS896 4.5 32.5 1.0
CB A:SER746 4.7 24.5 1.0
CB A:GLN743 4.9 17.7 1.0
CA A:ALA742 4.9 21.3 1.0
CB A:ALA900 5.0 32.2 1.0

Iodine binding site 7 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 7 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1007

b:96.3
occ:1.00
 CG2 A:VAL624 4.2 37.5 1.0
CB A:VAL624 4.2 41.2 1.0
CA A:GLY617 4.3 42.3 1.0
CG1 A:VAL624 4.3 39.0 1.0
O A:LEU616 4.4 56.3 1.0
N5 A:1IJ1009 4.7 31.2 1.0
N A:GLY617 4.7 53.4 1.0
C A:LEU616 4.7 54.0 1.0
C18 A:1IJ1009 4.7 19.7 1.0
CE1 A:PHE779 4.7 39.2 1.0
CD2 A:LEU616 4.8 78.7 1.0

Iodine binding site 8 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 8 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1008

b:122.8
occ:1.00
 O A:HOH1115 3.7 38.0 1.0
C A:GLY622 3.7 45.4 1.0
O A:GLY622 3.8 61.0 1.0
CA A:GLY622 3.9 50.7 1.0
N A:GLY619 3.9 82.1 1.0
CA A:GLY619 3.9 72.5 1.0
N A:GLY622 4.1 51.7 1.0
CG2 A:VAL624 4.2 37.5 1.0
N A:GLU623 4.2 45.0 1.0
CE A:LYS655 4.2 39.3 1.0
O A:HOH1186 4.5 37.0 1.0
CG A:LYS655 4.5 39.2 1.0
C A:GLU623 4.6 42.8 1.0
CA A:GLU623 4.6 43.4 1.0
O A:GLU623 4.6 37.0 1.0
C A:GLY619 4.6 67.8 1.0
CD A:LYS655 4.7 34.4 1.0
C A:GLU618 4.7 76.5 1.0

Iodine binding site 9 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 9 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1001

b:35.7
occ:1.00
 O A:HOH1184 3.5 21.9 1.0
N B:GLN841 3.8 26.3 1.0
CA B:PHE839 3.9 21.8 1.0
C B:PHE839 3.9 24.7 1.0
CB B:GLN841 3.9 26.2 1.0
NZ A:LYS671 4.1 37.5 1.0
CD A:LYS671 4.2 44.5 1.0
N B:GLY840 4.2 21.3 1.0
O B:PHE839 4.2 23.7 1.0
CG B:LEU842 4.2 30.3 1.0
CD1 A:ILE675 4.3 30.4 1.0
CA B:GLN841 4.3 27.6 1.0
CE A:LYS671 4.4 34.0 1.0
CG B:GLN841 4.5 22.3 1.0
CD2 B:LEU842 4.5 20.9 1.0
N B:LEU842 4.5 26.0 1.0
C B:GLN841 4.7 30.8 1.0
N B:PHE839 4.8 23.9 1.0
CB B:PHE839 4.8 23.8 1.0
CD1 B:PHE839 4.8 23.1 1.0
C B:GLY840 4.9 25.2 1.0
CD1 B:LEU842 5.0 28.8 1.0

Iodine binding site 10 out of 15 in 5say

Go back to Iodine Binding Sites List in 5say
Iodine binding site 10 out of 15 in the DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of DDR1, N-[2-[3-(2-Aminopyrimidin-5-Yl)Oxyphenyl]Ethyl]-3- (Trifluoromethoxy)Benzamide, 2.190A, P1211, Rfree=27.7% within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I1002

b:94.8
occ:1.00
 O B:SER893 3.7 33.1 1.0
CD B:ARG897 4.0 50.5 1.0
C B:SER893 4.0 34.0 1.0
NE B:ARG897 4.1 49.6 1.0
O B:HOH1124 4.1 40.5 1.0
CZ B:ARG897 4.2 46.6 1.0
NH2 B:ARG897 4.2 42.5 1.0
N B:GLN894 4.2 24.6 1.0
CA B:GLN894 4.3 35.0 1.0
CB B:SER893 4.3 29.7 1.0
CG B:GLN894 4.3 40.4 1.0
OG B:SER893 4.3 39.2 1.0
CB B:ARG897 4.4 28.8 1.0
CA B:SER893 4.7 28.4 1.0
CG B:ARG897 4.8 31.5 1.0
CB B:GLN894 4.9 26.0 1.0
NH1 B:ARG897 4.9 48.4 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 21:48:06 2024

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