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Iodine in PDB 5sax: DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form

Enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form

All present enzymatic activity of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form:
2.7.10.1;

Protein crystallography data

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form, PDB code: 5sax 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) 40.07 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.25, 73.76, 74.31, 90, 90, 90
R / Rfree (%) 20.9 / 25.4

Other elements in 5sax:

The structure of DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form 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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form (pdb code 5sax). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 8 binding sites of Iodine where determined in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form, PDB code: 5sax:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iodine binding site 1 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 1 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1001

b:78.7
occ:1.00
 CG A:ASP660 3.8 58.7 1.0
OD1 A:ASP660 3.9 53.2 1.0
N A:ASP660 3.9 46.5 1.0
CB A:ASP660 4.0 55.5 1.0
CD A:PRO659 4.0 47.2 1.0
CB A:PRO659 4.3 45.1 1.0
OD2 A:ASP660 4.3 66.7 1.0
CG A:PRO659 4.3 47.3 1.0
N A:PRO659 4.5 49.4 1.0
NH2 A:ARG658 4.5 73.2 1.0
CA A:ASP660 4.6 55.4 1.0
C A:PRO659 4.6 48.7 1.0
CA A:PRO659 4.7 44.4 1.0
CZ A:ARG658 4.7 72.4 1.0
CB A:ARG658 4.9 54.5 1.0

Iodine binding site 2 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 2 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1002

b:33.8
occ:1.00
 CD A:LYS671 4.2 31.1 1.0
NZ A:LYS671 4.2 35.2 1.0
CE A:LYS671 4.5 39.0 1.0
CD1 A:ILE675 4.5 37.9 1.0

Iodine binding site 3 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 3 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1003

b:50.9
occ:1.00
 N A:LEU718 3.5 40.2 1.0
CA A:GLN717 4.0 42.0 1.0
CG A:GLN717 4.2 44.7 1.0
CB A:LEU718 4.3 33.2 1.0
C A:GLN717 4.3 44.4 1.0
CD2 A:LEU833 4.3 46.8 1.0
CB A:GLN717 4.4 52.1 1.0
NH1 A:ARG835 4.4 41.1 1.0
CA A:LEU718 4.5 40.4 1.0
CZ A:ARG835 4.6 46.7 1.0
CD1 A:LEU833 4.6 33.0 1.0
CB A:LEU833 4.7 28.8 1.0
CG A:LEU833 4.8 35.0 1.0
NE A:ARG835 4.9 42.0 1.0
O A:HOH1204 4.9 41.1 1.0
NE2 A:GLN717 4.9 48.5 1.0
O A:HIS716 5.0 39.8 1.0
NH2 A:ARG835 5.0 34.1 1.0

Iodine binding site 4 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 4 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1004

b:64.8
occ:1.00
 OE1 A:GLN894 3.3 56.2 1.0
CG A:GLN894 3.6 49.0 1.0
CD1 A:LEU877 3.7 36.7 1.0
NH1 A:ARG880 3.8 45.1 1.0
CD A:GLN894 3.9 54.0 1.0
NE A:ARG880 3.9 52.1 1.0
CB A:PRO890 4.1 35.0 1.0
CG A:LEU877 4.2 42.6 1.0
O A:GLN894 4.2 42.7 1.0
CG A:PRO890 4.2 39.0 1.0
CZ A:ARG880 4.3 53.9 1.0
CD2 A:LEU895 4.4 35.7 1.0
CB A:PHE898 4.5 41.1 1.0
C A:GLN894 4.5 39.6 1.0
N A:LEU895 4.7 36.7 1.0
CA A:LEU895 4.7 36.1 1.0
CB A:GLN894 4.7 43.0 1.0
CD2 A:PHE898 4.8 43.6 1.0
CG A:PHE898 4.8 45.6 1.0
CB A:LEU877 4.9 41.9 1.0

Iodine binding site 5 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 5 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1005

b:82.2
occ:1.00
 O A:HOH1119 3.3 53.9 1.0
N A:LEU874 3.6 37.4 1.0
O A:HOH1189 3.8 42.4 1.0
CA A:GLY873 3.9 39.9 1.0
C A:GLY873 3.9 48.4 1.0
CZ A:PHE898 4.0 46.6 1.0
CE1 A:PHE898 4.2 42.6 1.0
CA A:LEU874 4.3 34.7 1.0
CB A:LEU874 4.3 37.2 1.0
N A:GLY873 4.4 36.8 1.0
CB A:PRO871 4.4 38.1 1.0
CA A:ALA903 4.4 39.2 1.0
O A:GLY873 4.8 40.5 1.0
CG A:PRO871 4.8 44.7 1.0
O A:ALA903 4.8 44.2 1.0
CB A:ALA903 4.9 39.1 1.0
O A:ASP902 5.0 44.8 1.0

Iodine binding site 6 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 6 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1006

b:85.0
occ:1.00
 NE2 A:HIS896 3.4 44.9 1.0
O A:HOH1116 3.4 46.4 1.0
CB A:ALA742 4.1 36.5 1.0
CD2 A:HIS896 4.1 36.7 1.0
C A:ALA742 4.1 35.6 1.0
N A:GLN743 4.2 33.0 1.0
CG A:GLN743 4.2 37.0 1.0
O A:ALA742 4.2 31.2 1.0
O A:HOH1232 4.3 52.1 1.0
CA A:GLN743 4.3 34.1 1.0
CE1 A:HIS896 4.4 48.5 1.0
CB A:SER746 4.8 34.5 1.0
CA A:ALA742 4.8 33.1 1.0
CB A:GLN743 4.9 34.0 1.0
CE1 A:HIS739 4.9 43.6 1.0
ND1 A:HIS739 4.9 40.4 1.0

Iodine binding site 7 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 7 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1007

b:87.3
occ:1.00
 O A:HOH1218 2.7 35.9 1.0
NZ A:LYS655 3.3 36.2 1.0
CE A:LYS655 3.7 42.3 1.0
O A:HOH1205 3.8 54.2 1.0
CD A:LYS655 3.9 41.7 1.0
N A:GLY619 4.0 62.3 1.0
CA A:GLY619 4.0 60.7 1.0
O A:GLY622 4.1 54.9 1.0
CD1 A:PHE779 4.1 36.6 1.0
CG2 A:VAL624 4.2 43.3 1.0
O A:PHE779 4.5 43.1 1.0
C A:GLY622 4.5 56.5 1.0
CG A:LYS655 4.8 43.1 1.0
CA A:PHE779 4.8 34.4 1.0
C A:GLU618 4.8 59.8 1.0
CE1 A:PHE779 4.9 34.3 1.0
CB A:PHE779 4.9 34.5 1.0
CA A:GLU623 5.0 55.3 1.0
O A:HOH1110 5.0 40.0 1.0
C8 A:1IM1009 5.0 32.5 1.0
N A:GLU623 5.0 49.9 1.0
C A:PHE779 5.0 38.2 1.0

Iodine binding site 8 out of 8 in 5sax

Go back to Iodine Binding Sites List in 5sax
Iodine binding site 8 out of 8 in the DDR1, 2-[3-(2-Pyridin-3-Ylethynyl)Phenyl]-N-[3-(Trifluoromethyl) Phenyl]Acetamide, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form


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, 1.902A, Second P212121 Form, Rfree=25.4%, Second Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I1008

b:105.9
occ:1.00
 C A:ASP681 3.7 35.9 1.0
N A:PRO682 3.7 38.3 1.0
O A:ASP681 3.8 35.1 1.0
O A:HOH1147 4.0 42.4 1.0
CA A:PRO682 4.0 39.6 1.0
N A:ASP681 4.0 34.7 1.0
CD A:PRO682 4.1 42.2 1.0
CA A:ASP681 4.2 39.5 1.0
O A:HOH1231 4.2 52.1 1.0
CG A:PRO682 4.4 40.6 1.0
C A:LYS680 4.6 42.2 1.0
CB A:PRO682 4.8 39.0 1.0
CD A:ARG686 4.8 52.0 1.0
NH1 A:ARG686 4.8 68.9 1.0
O A:HOH1144 4.9 38.5 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 21:47:27 2024

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