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Chlorine in PDB 7g3e: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm, PDB code: 7g3e was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.82 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.939, 91.59, 120.062, 90, 90, 90
R / Rfree (%) 17.4 / 20.7

Other elements in 7g3e:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm (pdb code 7g3e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm, PDB code: 7g3e:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g3e

Go back to Chlorine Binding Sites List in 7g3e
Chlorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:64.6
occ:1.00
 N A:ASN230 3.2 52.5 1.0
CA A:GLY229 3.6 36.5 1.0
NH1 A:ARG391 3.7 41.0 1.0
C A:GLY229 3.9 45.0 1.0
N A:SER231 3.9 53.2 1.0
CE A:LYS208 4.1 39.3 1.0
CA A:ASN230 4.2 58.4 1.0
CD1 A:LEU389 4.2 41.7 1.0
CG1 A:VAL385 4.3 41.9 1.0
CB A:ASN230 4.4 55.5 1.0
CG A:LYS208 4.4 32.6 1.0
C A:ASN230 4.5 58.2 1.0
CD2 A:LEU389 4.5 44.9 1.0
O A:SER231 4.5 47.6 1.0
CG A:LEU389 4.5 40.1 1.0
CZ A:ARG391 4.8 39.0 1.0
CD A:LYS208 4.8 35.8 1.0
CA A:SER231 5.0 46.8 1.0
N A:GLY229 5.0 29.3 1.0

Chlorine binding site 2 out of 2 in 7g3e

Go back to Chlorine Binding Sites List in 7g3e
Chlorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 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 5-Tert-Butyl-2- Methyl-4-[[3-(2-Oxa-7-Azaspiro[4.4]Nonane-7-Carbonyl)-1H-Pyrazol-5- Yl]Methoxy]Benzonitrile, I.E. Smiles CC1CC(C(CC1C#N)C(C)(C)C) OCC1=Cc(=NN1)C(=O)N1CC[C@]2(CCOC2)C1 with IC50=0.00824801 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl904

b:77.3
occ:1.00
 N A:PHE273 3.3 34.0 1.0
N A:PHE274 3.9 35.1 1.0
CB A:PHE273 4.0 32.4 1.0
CA A:THR272 4.0 43.8 1.0
CA A:PHE273 4.1 32.5 1.0
C A:THR272 4.2 36.8 1.0
CB A:THR272 4.3 55.5 1.0
CE2 A:TRP260 4.4 34.8 1.0
CD2 A:TRP260 4.5 30.4 1.0
C A:PHE273 4.5 37.4 1.0
NE1 A:TRP260 4.6 34.2 1.0
CG A:TRP260 4.7 31.8 1.0
CD1 A:TRP260 4.7 34.4 1.0
CZ2 A:TRP260 4.7 33.5 1.0
CB A:PHE274 4.7 40.1 1.0
CG2 A:THR272 4.8 54.4 1.0
CG A:PHE273 4.8 29.8 1.0
CD1 A:PHE273 4.9 31.1 1.0
CE3 A:TRP260 4.9 33.0 1.0
CD1 A:LEU78 4.9 79.3 1.0
CA A:PHE274 4.9 38.5 1.0
O A:GLY271 5.0 35.6 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: Sun Jul 13 01:04:12 2025

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