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Calcium in PDB 7g59: Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm, PDB code: 7g59 was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.96 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.521, 91.926, 120.213, 90, 90, 90
R / Rfree (%) 19.2 / 24.1

Other elements in 7g59:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm (pdb code 7g59). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm, PDB code: 7g59:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g59

Go back to Calcium Binding Sites List in 7g59
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:26.7
occ:1.00
 OD1 A:ASP747 2.2 27.4 1.0
O A:HOH1300 2.2 32.4 1.0
OD1 A:ASP743 2.3 30.5 1.0
OD1 A:ASP739 2.3 25.5 1.0
O A:LEU745 2.3 22.6 1.0
OD1 A:ASN741 2.4 26.6 1.0
CG A:ASP743 3.3 31.8 1.0
CG A:ASN741 3.4 31.7 1.0
CG A:ASP747 3.4 26.4 1.0
C A:LEU745 3.5 27.3 1.0
CG A:ASP739 3.5 27.6 1.0
OD2 A:ASP743 3.7 33.5 1.0
ND2 A:ASN741 3.8 31.0 1.0
N A:ASP747 3.9 23.6 1.0
CA A:ASP739 4.0 24.7 1.0
N A:LEU745 4.1 25.1 1.0
C A:ARG746 4.1 26.2 1.0
CA A:ASP747 4.1 24.7 1.0
CA A:LEU745 4.2 25.9 1.0
CB A:ASP739 4.2 26.8 1.0
OD2 A:ASP747 4.2 28.8 1.0
O A:ARG746 4.3 25.6 1.0
N A:ASP743 4.3 28.6 1.0
CB A:LEU745 4.4 28.9 1.0
CB A:ASP747 4.4 24.2 1.0
O A:PHE738 4.4 21.3 1.0
N A:ASN741 4.5 25.9 1.0
C A:ASP739 4.5 29.0 1.0
OD2 A:ASP739 4.5 27.1 1.0
CB A:ASP743 4.5 29.7 1.0
N A:ARG746 4.5 22.6 1.0
OE2 A:GLU751 4.6 47.0 1.0
CB A:ASN741 4.7 28.1 1.0
N A:TYR740 4.7 25.6 1.0
N A:TYR742 4.7 31.6 1.0
CA A:ARG746 4.7 24.7 1.0
N A:GLY744 4.8 26.1 1.0
CA A:ASP743 4.8 28.7 1.0
C A:ASN741 4.9 30.6 1.0
CA A:ASN741 4.9 29.6 1.0

Calcium binding site 2 out of 2 in 7g59

Go back to Calcium Binding Sites List in 7g59
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4-(2,2,2- Trifluoroethoxy)Phenyl]Methyl 2-(4,5,6,7-Tetrahydro-1H-Benzotriazole- 5-Carbonyl)-2,7-Diazaspiro[3.5]Nonane-7-Carboxylate, I.E. Smiles C1N(CC21CCN(CC2)C(=O)OCC1C(Cc(CC1)Occ(F)(F)F)F)C(=O)[C@H]1CCC2=C(C1) N=NN2 with IC50=0.211229 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:26.6
occ:1.00
 OG1 A:THR209 1.8 26.9 1.0
OD1 A:ASP171 1.8 28.3 1.0
NE2 A:HIS359 2.1 26.6 1.0
OD2 A:ASP358 2.1 29.9 1.0
CG A:ASP171 2.5 29.8 1.0
OD2 A:ASP171 2.7 33.0 1.0
CG A:ASP358 2.9 26.7 1.0
CB A:THR209 3.0 28.8 1.0
CD2 A:HIS359 3.0 27.3 1.0
CE1 A:HIS359 3.0 27.3 1.0
OD1 A:ASP358 3.1 23.9 1.0
CA A:THR209 3.4 28.9 1.0
CG2 A:THR209 3.5 29.0 1.0
N A:THR209 3.9 29.9 1.0
CB A:ASP171 3.9 27.5 1.0
ND1 A:HIS359 4.1 26.7 1.0
CG A:HIS359 4.1 29.3 1.0
O A:HOH1013 4.1 45.7 1.0
N A:GLY172 4.1 28.8 1.0
CA A:ASP171 4.3 29.0 1.0
CB A:ASP358 4.3 27.5 1.0
CE1 A:HIS474 4.4 24.3 1.0
C14 A:YFX901 4.4 52.2 1.0
OD1 A:ASP311 4.4 35.4 1.0
CG A:ASP311 4.4 32.8 1.0
C A:ASP171 4.6 28.3 1.0
NE2 A:HIS474 4.6 25.4 1.0
C A:LYS208 4.7 31.9 1.0
OD2 A:ASP311 4.7 31.8 1.0
ZN A:ZN904 4.7 32.6 1.0
C A:THR209 4.8 30.9 1.0
OXT A:ACT910 4.8 40.5 1.0
CB A:ASP311 4.9 29.2 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 15:49:18 2025

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