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Iodine in PDB 5saw: DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%

Enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%

All present enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%, PDB code: 5saw 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) 44.07 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.63, 61.64, 116.14, 90, 90, 90
R / Rfree (%) 19.9 / 22.6

Other elements in 5saw:

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% (pdb code 5saw). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%, PDB code: 5saw:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 1 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:20.4
occ:1.00
 O A:HOH1291 3.5 18.9 1.0
CA A:PHE839 3.8 13.1 1.0
N A:GLN841 3.9 15.1 1.0
C A:PHE839 3.9 14.4 1.0
CB A:GLN841 4.0 13.4 1.0
N A:GLY840 4.1 15.7 1.0
CG A:LEU842 4.3 19.3 1.0
O A:PHE839 4.3 13.9 1.0
CA A:GLN841 4.4 14.1 1.0
CG A:GLN841 4.5 14.6 1.0
N A:LEU842 4.7 14.1 1.0
CD1 A:LEU842 4.7 19.8 1.0
N A:PHE839 4.7 14.3 1.0
O A:HOH1248 4.7 19.4 1.0
CB A:PHE839 4.7 13.7 1.0
C A:GLN841 4.7 15.8 1.0
CD1 A:PHE839 4.8 15.2 1.0
C A:GLY840 4.9 15.3 1.0
O A:HOH1140 5.0 23.2 1.0

Iodine binding site 2 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 2 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:28.0
occ:1.00
 N A:LEU718 3.6 19.7 1.0
CA A:GLN717 3.9 19.1 1.0
CB A:GLN717 4.1 23.3 1.0
NH1 A:ARG835 4.2 28.2 1.0
CD2 A:LEU833 4.2 20.2 1.0
CG A:GLN717 4.2 27.4 1.0
C A:GLN717 4.3 22.2 1.0
CZ A:ARG835 4.4 22.5 1.0
CB A:LEU718 4.4 19.3 1.0
CD1 A:LEU833 4.4 17.7 1.0
CA A:LEU718 4.6 21.6 1.0
CG A:LEU833 4.6 19.2 1.0
CB A:LEU833 4.7 14.9 1.0
NE A:ARG835 4.7 25.8 1.0
O A:HIS716 4.8 22.7 1.0
NH2 A:ARG835 4.8 18.9 1.0
O A:HOH1221 4.9 20.1 1.0

Iodine binding site 3 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 3 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:31.7
occ:1.00
 NE2 A:GLN894 3.3 39.4 1.0
NH1 A:ARG880 3.7 27.9 1.0
NE A:ARG880 3.8 24.0 1.0
CG A:GLN894 3.8 32.5 1.0
CD1 A:LEU877 4.0 23.4 1.0
CB A:PRO890 4.0 19.7 1.0
CD A:GLN894 4.1 33.6 1.0
CG A:PRO890 4.1 24.9 1.0
CD2 A:LEU895 4.2 14.9 1.0
CZ A:ARG880 4.2 23.6 1.0
CG A:LEU877 4.3 20.5 1.0
CD2 A:PHE898 4.3 27.6 1.0
CB A:PHE898 4.4 19.5 1.0
O A:GLN894 4.4 20.4 1.0
C A:GLN894 4.5 18.8 1.0
CG A:PHE898 4.5 27.6 1.0
CA A:LEU895 4.6 16.6 1.0
N A:LEU895 4.6 18.6 1.0
CB A:GLN894 4.8 23.7 1.0
CG A:LEU895 4.8 17.3 1.0
CD A:ARG880 4.9 18.8 1.0
CB A:LEU877 5.0 17.4 1.0

Iodine binding site 4 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 4 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:53.5
occ:1.00
 O A:HOH1119 3.2 35.3 1.0
N A:LEU874 3.7 17.7 1.0
C A:GLY873 4.0 19.7 1.0
CA A:GLY873 4.1 21.8 1.0
CZ A:PHE898 4.3 32.1 1.0
CA A:LEU874 4.4 15.5 1.0
CB A:LEU874 4.5 17.1 1.0
CE1 A:PHE898 4.5 29.1 1.0
O A:GLY873 4.7 20.3 1.0
N A:GLY873 4.7 20.8 1.0
CB A:PRO871 4.8 23.4 1.0
O A:HOH1234 4.9 29.9 1.0

Iodine binding site 5 out of 10 in 5saw

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Iodine binding site 5 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:49.1
occ:1.00
 OG A:SER608 3.0 29.1 1.0
CB A:SER608 3.5 27.7 1.0
O A:HOH1336 3.6 33.1 1.0
O A:HOH1300 3.9 27.9 1.0
N A:SER608 3.9 22.3 1.0
O A:HOH1258 4.0 26.3 1.0
CA A:SER608 4.4 24.1 1.0
N A:ARG607 4.4 19.9 1.0
CB A:PRO606 4.5 20.2 1.0
CA A:PRO606 4.5 18.1 1.0
C A:PRO606 4.6 17.7 1.0
O A:HOH1189 4.8 23.5 1.0
C A:ARG607 5.0 19.4 1.0

Iodine binding site 6 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 6 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1007

b:38.7
occ:1.00
 O A:HOH1219 3.8 16.8 1.0
CD A:ARG749 4.2 21.8 1.0
CB A:SER893 4.2 16.2 1.0
CG A:ARG749 4.2 18.2 1.0
CG2 A:THR753 4.6 19.1 1.0
OG A:SER893 4.9 21.4 1.0
O A:HOH1226 4.9 24.3 1.0
NE A:ARG749 5.0 33.8 1.0

Iodine binding site 7 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 7 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1008

b:65.7
occ:1.00
 N A:SER733 3.5 21.2 1.0
OG A:SER733 3.9 24.2 1.0
CZ A:PHE772 3.9 33.1 1.0
CA A:ILE732 4.0 21.5 1.0
CB A:SER733 4.1 27.3 1.0
CB A:MET736 4.1 26.9 1.0
CE2 A:PHE772 4.2 28.1 1.0
C A:ILE732 4.2 21.5 1.0
CG A:MET736 4.2 27.0 1.0
CE A:MET736 4.2 32.7 1.0
OE2 A:GLU719 4.3 45.1 1.0
O A:HOH1153 4.3 34.6 1.0
O A:THR731 4.3 26.0 1.0
CA A:SER733 4.4 22.7 1.0
CG1 A:ILE732 4.5 22.7 1.0
CE1 A:PHE772 4.7 29.8 1.0
CB A:ILE732 4.8 21.0 1.0
N A:ILE732 4.9 22.8 1.0
C A:THR731 4.9 24.3 1.0

Iodine binding site 8 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 8 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1009

b:89.0
occ:1.00
 NH2 A:ARG897 3.2 36.5 1.0
O A:HOH1232 3.6 21.8 1.0
NE A:ARG897 3.7 39.2 1.0
CZ A:ARG897 3.9 43.0 1.0
CB A:SER893 4.2 16.2 1.0
O A:SER893 4.4 20.6 1.0
C A:SER893 4.8 18.1 1.0
OG A:SER893 4.9 21.4 1.0
CA A:SER893 4.9 18.2 1.0
CD A:ARG897 4.9 41.3 1.0

Iodine binding site 9 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 9 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1010

b:59.4
occ:1.00
 O A:HOH1125 3.4 33.2 1.0
NE2 A:HIS896 3.4 28.6 1.0
O A:HOH1257 3.8 27.1 1.0
CB A:ALA742 4.0 14.2 1.0
C A:ALA742 4.0 14.2 1.0
CD2 A:HIS896 4.0 18.5 1.0
N A:GLN743 4.1 13.2 1.0
O A:ALA742 4.1 12.8 1.0
CG A:GLN743 4.1 15.4 1.0
CA A:GLN743 4.2 13.1 1.0
CB A:SER746 4.5 17.2 1.0
CE1 A:HIS896 4.6 28.6 1.0
CA A:ALA742 4.7 16.0 1.0
CB A:GLN743 4.8 15.0 1.0
CB A:ALA900 4.8 23.9 1.0
CE1 A:HIS739 4.9 18.8 1.0
ND1 A:HIS739 4.9 18.9 1.0
OG A:SER746 4.9 16.8 1.0

Iodine binding site 10 out of 10 in 5saw

Go back to Iodine Binding Sites List in 5saw
Iodine binding site 10 out of 10 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6%


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.601A, P212121, Rfree=22.6% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1011

b:106.1
occ:1.00
 N A:SER631 3.4 26.2 1.0
ND1 A:HIS648 3.6 59.6 1.0
N A:PRO649 3.8 42.6 1.0
C A:HIS648 3.9 45.0 1.0
CB A:HIS648 4.0 55.2 1.0
CA A:PRO649 4.0 38.6 1.0
CD A:PRO649 4.0 49.6 1.0
O A:HIS648 4.1 46.5 1.0
CA A:SER631 4.1 29.7 1.0
CA A:ASP630 4.2 27.5 1.0
CG A:HIS648 4.2 61.7 1.0
C A:ASP630 4.3 24.1 1.0
CB A:PRO649 4.4 38.6 1.0
CB A:ASP630 4.5 28.8 1.0
OD1 A:ASP630 4.5 37.7 1.0
CA A:HIS648 4.6 51.0 1.0
CE1 A:HIS648 4.6 60.2 1.0
CB A:SER631 4.7 34.2 1.0
CG A:PRO649 4.8 40.1 1.0
CG A:ASP630 4.9 34.6 1.0
CD A:PRO632 5.0 21.7 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 21:47:23 2024

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