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Chlorine in PDB 7g3q: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm, PDB code: 7g3q was solved by M.Stihle, J.Benz, D.Hunziker, L.Green, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.94 / 1.78
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.014, 91.722, 120.119, 90, 90, 90
R / Rfree (%) 18 / 22.5

Other elements in 7g3q:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm (pdb code 7g3q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm, PDB code: 7g3q:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 7g3q

Go back to Chlorine Binding Sites List in 7g3q
Chlorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:38.5
occ:0.50
 CL1 A:YO8901 0.0 38.5 0.5
C2 A:YO8901 1.6 23.9 1.0
CL A:CL909 2.1 37.8 0.5
C13 A:YO8901 2.5 22.6 1.0
C3 A:YO8901 2.6 22.9 1.0
C4 A:YO8901 3.0 22.1 1.0
OG A:SER169 3.5 31.9 1.0
C12 A:YO8901 3.7 21.6 1.0
N5 A:YO8901 3.8 25.8 1.0
C6 A:YO8901 3.8 23.4 1.0
CB A:SER169 3.8 22.7 1.0
CG2 A:ILE167 3.9 16.5 1.0
CB A:ALA304 3.9 19.6 1.0
O A:HOH1004 4.1 21.8 1.0
CD2 A:PHE273 4.3 18.1 1.0
C7 A:YO8901 4.3 23.1 1.0
CD2 A:LEU216 4.5 25.0 1.0
CB A:ILE167 4.6 17.1 1.0
CD2 A:LEU213 4.7 21.2 1.0
CE2 A:PHE273 4.8 18.6 1.0
O14 A:YO8901 4.8 22.1 1.0
O A:PHE305 4.9 23.8 1.0
O A:ILE167 4.9 20.8 1.0

Chlorine binding site 2 out of 3 in 7g3q

Go back to Chlorine Binding Sites List in 7g3q
Chlorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl908

b:46.7
occ:1.00
 N A:ASN230 3.2 27.8 1.0
NH1 A:ARG391 3.5 35.4 1.0
CA A:GLY229 3.5 23.9 1.0
N A:SER231 3.8 39.0 1.0
C A:GLY229 3.8 25.7 1.0
CA A:ASN230 4.1 34.1 1.0
OG A:SER231 4.1 47.4 1.0
O A:SER231 4.2 43.6 1.0
CE A:LYS208 4.3 32.2 1.0
CB A:ASN230 4.3 32.5 1.0
C A:ASN230 4.4 36.3 1.0
CG1 A:VAL385 4.4 30.6 1.0
CD1 A:LEU389 4.4 34.1 1.0
CZ A:ARG391 4.4 31.7 1.0
NH2 A:ARG391 4.5 31.0 1.0
CG A:LYS208 4.6 23.6 1.0
CD2 A:LEU389 4.8 33.8 1.0
CA A:SER231 4.8 40.1 1.0
CG A:LEU389 4.8 28.8 1.0
N A:GLY229 4.9 21.2 1.0
CD A:LYS208 5.0 26.2 1.0
O A:GLY229 5.0 26.3 1.0
C A:SER231 5.0 37.4 1.0

Chlorine binding site 3 out of 3 in 7g3q

Go back to Chlorine Binding Sites List in 7g3q
Chlorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-N-(1,1-Dioxothietan-3-Yl)-3- Methylimidazole-4-Carboxamide, I.E. Smiles CLC1C(C#N)Cc(C(C)(C)C) C(C1)OCC1=Nc=C(C(=O)NC2CS(=O)(=O)C2)N1C with IC50=0.0049749 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl909

b:37.8
occ:0.50
 CL1 A:YO8901 2.1 38.5 0.5
OG A:SER169 2.5 31.9 1.0
O A:PHE305 2.8 23.8 1.0
O A:HOH1004 3.1 21.8 1.0
CB A:SER169 3.3 22.7 1.0
C2 A:YO8901 3.3 23.9 1.0
C A:PHE305 3.4 20.9 1.0
C13 A:YO8901 3.4 22.6 1.0
CB A:ALA304 3.4 19.6 1.0
O A:ILE167 3.6 20.8 1.0
N A:PHE305 3.6 20.3 1.0
N A:SER169 3.6 18.7 1.0
CA A:SER169 4.0 22.0 1.0
N A:TYR306 4.1 17.1 1.0
CA A:ALA304 4.1 19.4 1.0
C A:ALA304 4.1 18.0 1.0
CG2 A:ILE167 4.1 16.5 1.0
CA A:TYR306 4.2 19.3 1.0
CB A:TYR306 4.2 20.1 1.0
CA A:PHE305 4.2 20.4 1.0
C A:ILE167 4.3 20.2 1.0
C3 A:YO8901 4.5 22.9 1.0
CB A:ILE167 4.6 17.1 1.0
C A:PHE168 4.7 17.5 1.0
C12 A:YO8901 4.7 21.6 1.0
O A:SER169 4.9 24.0 1.0
CA A:PHE168 4.9 17.1 1.0
N A:PHE168 4.9 16.8 1.0
O A:PHE273 4.9 32.9 1.0
C A:SER169 5.0 22.9 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 16:53:09 2025

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