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Chlorine in PDB 7g4w: Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm, PDB code: 7g4w 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) 45.79 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.98, 91.582, 119.383, 90, 90, 90
R / Rfree (%) 19.3 / 23.4

Other elements in 7g4w:

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Potassium (K) 1 atom
Calcium (Ca) 1 atom
Sodium (Na) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm (pdb code 7g4w). 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm, PDB code: 7g4w:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7g4w

Go back to Chlorine Binding Sites List in 7g4w
Chlorine binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:43.9
occ:1.00
 CL41 A:YEH901 0.0 43.9 1.0
C38 A:YEH901 1.7 32.9 1.0
C37 A:YEH901 2.6 31.9 1.0
C39 A:YEH901 2.7 34.4 1.0
CB A:LEU216 3.7 18.9 1.0
C36 A:YEH901 3.9 32.0 1.0
C40 A:YEH901 4.0 32.3 1.0
N A:ALA217 4.0 19.9 1.0
C A:LEU216 4.1 19.1 1.0
CG2 A:ILE167 4.2 22.4 1.0
CA A:ALA217 4.2 19.1 1.0
CD1 A:ILE167 4.3 21.7 1.0
CE2 A:PHE273 4.4 31.0 1.0
C35 A:YEH901 4.4 31.8 1.0
CE A:MET512 4.4 22.1 1.0
O A:LEU216 4.5 20.3 1.0
CB A:ALA217 4.5 21.1 1.0
O A:LEU213 4.5 20.2 1.0
CA A:LEU216 4.6 18.2 1.0
CD2 A:PHE273 4.7 30.9 1.0
CD1 A:LEU216 4.7 21.6 1.0
CG A:LEU216 4.8 19.8 1.0
SD A:MET512 4.9 25.7 1.0

Chlorine binding site 2 out of 2 in 7g4w

Go back to Chlorine Binding Sites List in 7g4w
Chlorine binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 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 (6-Chloro-9H- Carbazol-2-Yl)-[(1R,2S,6R,7S)-4,9-Diazatricyclo[5.3.0.0-2,6]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)C1CCC2-C3C(NC2C1)Ccc(C3)Cl with IC50=0.26635 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl908

b:44.7
occ:1.00
 N A:ASN230 3.1 32.3 1.0
NH1 A:ARG391 3.5 27.5 1.0
CA A:GLY229 3.5 26.4 1.0
N A:SER231 3.6 32.5 1.0
C A:GLY229 3.8 29.1 1.0
CA A:ASN230 4.1 32.5 1.0
O A:SER231 4.1 33.9 1.0
CE A:LYS208 4.2 30.9 1.0
CG1 A:VAL385 4.3 24.6 1.0
CB A:ASN230 4.3 34.9 1.0
C A:ASN230 4.3 35.1 1.0
CD1 A:LEU389 4.5 29.8 1.0
CG A:LYS208 4.5 27.1 1.0
CA A:SER231 4.6 33.1 1.0
CZ A:ARG391 4.6 25.4 1.0
CB A:SER231 4.6 35.5 1.0
CD2 A:LEU389 4.6 35.2 1.0
O A:HOH1202 4.7 36.0 1.0
CG A:LEU389 4.7 30.5 1.0
NH2 A:ARG391 4.8 27.1 1.0
N A:GLY229 4.8 21.9 1.0
C A:SER231 4.8 31.1 1.0
O A:GLY229 4.9 29.1 1.0
CD A:LYS208 4.9 30.1 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 16:57:04 2025

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