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Chlorine in PDB 7g5r: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.89 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.288, 91.722, 120.027, 90, 90, 90
R / Rfree (%) 20 / 25

Other elements in 7g5r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Fluorine (F) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm (pdb code 7g5r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r:

Chlorine binding site 1 out of 1 in 7g5r

Go back to Chlorine Binding Sites List in 7g5r
Chlorine binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:48.2
occ:1.00
 N A:ASN230 3.3 36.5 1.0
NH1 A:ARG391 3.3 28.7 1.0
CA A:GLY229 3.4 30.9 1.0
C A:GLY229 3.8 32.4 1.0
N A:SER231 3.9 38.1 1.0
CD1 A:LEU389 4.2 34.9 1.0
CG1 A:VAL385 4.3 30.6 1.0
CA A:ASN230 4.3 38.3 1.0
O A:SER231 4.3 36.5 1.0
CE A:LYS208 4.3 35.1 1.0
CG A:LYS208 4.5 31.2 1.0
CZ A:ARG391 4.5 28.7 1.0
CB A:ASN230 4.5 36.1 1.0
C A:ASN230 4.6 41.4 1.0
CB A:SER231 4.6 38.3 1.0
CD2 A:LEU389 4.6 36.1 1.0
CG A:LEU389 4.7 35.0 1.0
CA A:SER231 4.7 36.7 1.0
N A:GLY229 4.8 27.8 1.0
CD A:LYS208 4.8 33.0 1.0
NH2 A:ARG391 4.9 32.3 1.0
O A:GLY229 5.0 32.7 1.0
O A:VAL228 5.0 26.4 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 01:10:47 2025

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