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Calcium in PDB 7g4b: Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm, PDB code: 7g4b 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) 49.00 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.398, 91.995, 120.378, 90, 90, 90
R / Rfree (%) 19.8 / 24.3

Other elements in 7g4b:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Potassium (K) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm (pdb code 7g4b). 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- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm, PDB code: 7g4b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4b

Go back to Calcium Binding Sites List in 7g4b
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 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- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:25.1
occ:1.00
 OD1 A:ASP743 2.2 27.6 1.0
O A:HOH1316 2.3 32.1 1.0
OD1 A:ASN741 2.3 28.5 1.0
OD1 A:ASP747 2.3 26.1 1.0
O A:LEU745 2.4 25.9 1.0
OD1 A:ASP739 2.4 25.4 1.0
CG A:ASP743 3.3 26.2 1.0
CG A:ASN741 3.3 28.1 1.0
CG A:ASP739 3.5 24.6 1.0
C A:LEU745 3.5 25.9 1.0
CG A:ASP747 3.6 26.8 1.0
OD2 A:ASP743 3.7 29.2 1.0
ND2 A:ASN741 3.7 27.8 1.0
N A:ASP747 4.0 28.1 1.0
CA A:ASP739 4.0 24.7 1.0
C A:ARG746 4.1 28.0 1.0
N A:LEU745 4.1 24.8 1.0
CA A:ASP747 4.2 26.9 1.0
O A:ARG746 4.2 27.9 1.0
N A:ASP743 4.2 26.6 1.0
CA A:LEU745 4.2 25.8 1.0
CB A:ASP739 4.2 25.5 1.0
OD2 A:ASP747 4.4 26.4 1.0
N A:ASN741 4.4 27.2 1.0
OD2 A:ASP739 4.4 23.9 1.0
CB A:LEU745 4.4 26.8 1.0
C A:ASP739 4.5 28.0 1.0
O A:PHE738 4.5 21.2 1.0
CB A:ASP747 4.5 26.7 1.0
CB A:ASP743 4.5 26.8 1.0
N A:ARG746 4.5 25.8 1.0
CB A:ASN741 4.6 27.2 1.0
N A:TYR742 4.7 29.8 1.0
N A:TYR740 4.7 26.9 1.0
CA A:ASP743 4.8 26.3 1.0
CA A:ARG746 4.8 27.9 1.0
CA A:ASN741 4.8 28.1 1.0
C A:ASN741 4.8 29.5 1.0
N A:GLY744 4.9 26.2 1.0
OE2 A:GLU751 4.9 43.1 1.0

Calcium binding site 2 out of 2 in 7g4b

Go back to Calcium Binding Sites List in 7g4b
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Fluoro-4- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 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- (Trifluoromethyl)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)C(F)(F)F)F)C(=O) [C@H]1CCC2=C(C1)N=NN2 with IC50=0.103944 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:24.1
occ:1.00
 OG1 A:THR209 1.7 22.7 1.0
OD1 A:ASP171 1.8 31.8 1.0
NE2 A:HIS359 2.0 22.2 1.0
OD2 A:ASP358 2.2 28.4 1.0
CG A:ASP171 2.6 31.7 1.0
OD2 A:ASP171 2.8 35.3 1.0
CE1 A:HIS359 2.9 21.6 1.0
CB A:THR209 2.9 25.0 1.0
CD2 A:HIS359 3.0 21.9 1.0
CG A:ASP358 3.0 26.0 1.0
OD1 A:ASP358 3.2 21.7 1.0
CA A:THR209 3.4 26.0 1.0
CG2 A:THR209 3.5 26.1 1.0
N A:THR209 3.9 27.6 1.0
ND1 A:HIS359 4.0 21.3 1.0
CB A:ASP171 4.0 28.6 1.0
CG A:HIS359 4.0 22.5 1.0
C14 A:YOC901 4.2 47.3 0.5
N A:GLY172 4.3 25.8 1.0
C14 A:YOC901 4.3 46.2 0.5
CA A:ASP171 4.3 27.7 1.0
OD1 A:ASP311 4.3 30.7 1.0
O A:HOH1002 4.3 38.1 1.0
CE1 A:HIS474 4.4 27.3 1.0
CG A:ASP311 4.4 28.2 1.0
CB A:ASP358 4.5 23.9 1.0
NE2 A:HIS474 4.5 26.8 1.0
ZN A:ZN902 4.6 31.1 1.0
C A:ASP171 4.7 25.8 1.0
C A:LYS208 4.7 30.1 1.0
C A:THR209 4.7 27.0 1.0
CB A:ASP311 4.7 28.4 1.0
OD2 A:ASP311 4.7 26.8 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 15:43:10 2025

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