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Calcium in PDB 7g33: Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm, PDB code: 7g33 was solved by M.Stihle, J.Benz, D.Hunziker, J.Plancher, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.81 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.176, 91.747, 119.809, 90, 90, 90
R / Rfree (%) 18.5 / 22.2

Other elements in 7g33:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm (pdb code 7g33). 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm, PDB code: 7g33:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g33

Go back to Calcium Binding Sites List in 7g33
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:30.0
occ:0.50
 OD1 A:ASP171 1.8 20.9 1.0
O A:HOH1079 2.0 23.7 1.0
OD2 A:ASP358 2.2 17.7 1.0
NE2 A:HIS359 2.2 14.1 1.0
CG A:ASP171 2.8 19.8 1.0
CG2 A:THR209 3.0 20.2 1.0
CG A:ASP358 3.0 16.8 1.0
CE1 A:HIS359 3.1 15.2 1.0
CD2 A:HIS359 3.2 14.7 1.0
OG1 A:THR209 3.2 26.1 1.0
CB A:THR209 3.3 19.7 1.0
OD2 A:ASP171 3.4 25.8 1.0
CA A:THR209 3.4 15.9 1.0
OD1 A:ASP358 3.4 16.1 1.0
N A:THR209 4.1 14.2 1.0
CB A:ASP171 4.1 16.4 1.0
N A:GLY172 4.1 13.3 1.0
OD1 A:ASP311 4.1 18.9 1.0
ND1 A:HIS359 4.2 15.0 1.0
CG A:HIS359 4.3 13.7 1.0
CA A:ASP171 4.3 15.5 1.0
CB A:ASP358 4.3 15.2 1.0
CG A:ASP311 4.4 16.1 1.0
CE1 A:HIS474 4.4 15.4 1.0
C13 A:XHQ902 4.5 28.7 1.0
ZN A:ZN905 4.5 16.7 1.0
C A:THR209 4.6 15.7 1.0
C A:ASP171 4.6 14.5 1.0
NE2 A:HIS474 4.6 15.1 1.0
OD2 A:ASP311 4.7 20.9 1.0
N18 A:XHQ902 4.8 20.2 1.0
C A:LYS208 4.9 15.1 1.0
C17 A:XHQ902 4.9 24.1 1.0
O A:THR209 4.9 15.0 1.0
CB A:ASP311 4.9 14.8 1.0
CA A:GLY172 5.0 12.3 1.0
OH A:TYR306 5.0 36.4 1.0

Calcium binding site 2 out of 2 in 7g33

Go back to Calcium Binding Sites List in 7g33
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 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 (3,5- Dichlorophenyl)Methyl 7-(3H-Benzotriazole-5-Carbonylamino)-5-Oxa-2- Azaspiro[3.4]Octane-2-Carboxylate, I.E. Smiles C12(C[C@@H](CO1) Nc(=O)C1CC3C(CC1)N=NN3)Cn(C2)C(=O)OCC1CC(Cc(C1)Cl)Cl with IC50=0.00754101 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:13.6
occ:1.00
 OD1 A:ASP747 2.3 15.3 1.0
O A:LEU745 2.3 13.3 1.0
OD1 A:ASN741 2.3 16.7 1.0
O A:HOH1505 2.3 17.2 1.0
OD1 A:ASP739 2.4 12.9 1.0
OD1 A:ASP743 2.4 15.1 1.0
CG A:ASP743 3.3 16.8 1.0
CG A:ASN741 3.4 18.0 1.0
C A:LEU745 3.5 12.2 1.0
CG A:ASP739 3.5 13.2 1.0
CG A:ASP747 3.5 15.7 1.0
OD2 A:ASP743 3.8 19.0 1.0
ND2 A:ASN741 3.9 19.9 1.0
N A:ASP747 3.9 13.3 1.0
CA A:ASP739 3.9 13.0 1.0
C A:ARG746 4.1 14.0 1.0
N A:LEU745 4.1 12.7 1.0
CA A:ASP747 4.1 13.3 1.0
O A:ARG746 4.2 14.7 1.0
CB A:ASP739 4.2 12.9 1.0
CA A:LEU745 4.2 12.8 1.0
N A:ASP743 4.3 13.9 1.0
OD2 A:ASP739 4.4 13.1 1.0
OD2 A:ASP747 4.4 14.7 1.0
CB A:ASP747 4.4 13.5 1.0
C A:ASP739 4.4 13.6 1.0
O A:PHE738 4.5 11.2 1.0
N A:ASN741 4.5 13.5 1.0
CB A:LEU745 4.5 13.1 1.0
N A:ARG746 4.5 12.6 1.0
CB A:ASP743 4.6 15.6 1.0
OE2 A:GLU751 4.6 26.3 1.0
N A:TYR740 4.7 12.4 1.0
O A:HOH1460 4.7 28.5 1.0
CB A:ASN741 4.7 15.8 1.0
CA A:ARG746 4.8 13.1 1.0
N A:TYR742 4.8 14.7 1.0
CA A:ASP743 4.8 13.7 1.0
N A:GLY744 4.9 14.0 1.0
C A:ASN741 4.9 16.0 1.0
CA A:ASN741 4.9 14.3 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 15:35:20 2025

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