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Calcium in PDB 7g46: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm, PDB code: 7g46 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) 45.58 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.858, 91.156, 118.324, 90, 90, 90
R / Rfree (%) 20.1 / 24.4

Other elements in 7g46:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 2 atoms
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm (pdb code 7g46). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm, PDB code: 7g46:

Calcium binding site 1 out of 1 in 7g46

Go back to Calcium Binding Sites List in 7g46
Calcium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 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 [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-[(5R)-4,5,6,7-Tetrahydro- 1H-Benzotriazole-5-Carbonyl]-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2) C(=O)OCC1CCC(CC1)Oc(F)(F)F)C(=O)[C@@H]1CCC2=C(C1)N=NN2 with IC50=0.00614797 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:18.7
occ:1.00
 OD1 A:ASN741 2.2 19.7 1.0
OD1 A:ASP739 2.3 18.0 1.0
O A:LEU745 2.3 17.4 1.0
OD1 A:ASP747 2.3 18.5 1.0
OD1 A:ASP743 2.3 19.8 1.0
O A:HOH1284 2.4 22.1 1.0
CG A:ASP743 3.3 20.1 1.0
CG A:ASN741 3.3 21.4 1.0
C A:LEU745 3.4 18.8 1.0
CG A:ASP739 3.4 18.4 1.0
CG A:ASP747 3.5 19.3 1.0
OD2 A:ASP743 3.6 20.2 1.0
ND2 A:ASN741 3.8 21.7 1.0
N A:ASP747 3.9 18.8 1.0
CA A:ASP739 4.0 18.5 1.0
N A:LEU745 4.0 17.6 1.0
C A:ARG746 4.1 20.0 1.0
CA A:LEU745 4.1 17.7 1.0
CA A:ASP747 4.2 19.4 1.0
CB A:ASP739 4.2 17.9 1.0
N A:ASP743 4.3 18.8 1.0
O A:ARG746 4.3 20.1 1.0
OD2 A:ASP747 4.3 21.1 1.0
OD2 A:ASP739 4.3 19.1 1.0
N A:ARG746 4.4 18.7 1.0
CB A:LEU745 4.4 18.0 1.0
C A:ASP739 4.4 18.9 1.0
CB A:ASP747 4.4 18.2 1.0
O A:PHE738 4.5 17.9 1.0
N A:ASN741 4.5 19.2 1.0
CB A:ASP743 4.5 18.6 1.0
CB A:ASN741 4.7 19.7 1.0
N A:TYR742 4.7 20.5 1.0
CA A:ARG746 4.7 20.0 1.0
N A:TYR740 4.7 18.9 1.0
N A:GLY744 4.8 18.0 1.0
CA A:ASP743 4.8 19.4 1.0
C A:ASN741 4.8 20.7 1.0
CA A:ASN741 4.9 19.9 1.0
OE2 A:GLU751 4.9 30.6 1.0
O A:HOH1327 5.0 38.5 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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