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Sodium 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
Calcium (Ca) 1 atom
Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where 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:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g46

Go back to Sodium Binding Sites List in 7g46
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na904

b:29.9
occ:1.00
 OG A:SER807 2.3 26.5 1.0
O A:SER804 2.3 22.6 1.0
O A:HOH1214 2.4 27.3 1.0
O A:HOH1352 2.5 33.2 1.0
O A:HOH1279 2.6 30.1 1.0
O A:ASN801 2.7 24.6 1.0
C A:SER804 3.4 23.7 1.0
CB A:SER807 3.4 29.4 1.0
C A:ASN801 3.6 24.1 1.0
CA A:ASP802 4.0 25.3 1.0
N A:SER807 4.0 28.4 1.0
CA A:CYS805 4.1 29.4 1.0
N A:ASP802 4.1 24.1 1.0
N A:CYS805 4.1 25.9 1.0
O A:ASP802 4.2 24.1 1.0
CA A:SER807 4.2 29.6 1.0
C A:CYS805 4.3 30.6 1.0
C A:ASP802 4.3 24.8 1.0
O A:HOH1126 4.3 39.7 1.0
O A:CYS805 4.3 31.6 1.0
CA A:SER804 4.4 22.0 1.0
N A:SER804 4.4 22.8 1.0
CB A:ASN801 4.6 23.9 1.0
CA A:ASN801 4.6 24.4 1.0
O A:HOH1263 4.7 32.5 1.0
CB A:SER804 4.8 22.5 1.0
OD1 A:ASP802 4.8 29.5 1.0
N A:ASN806 4.9 30.9 1.0
C A:SER807 4.9 31.1 1.0

Sodium binding site 2 out of 2 in 7g46

Go back to Sodium Binding Sites List in 7g46
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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:Na906

b:17.5
occ:1.00
 O A:ASP672 2.1 25.9 1.0
O A:TYR669 2.2 28.7 1.0
O A:HOH1278 2.3 29.9 1.0
O A:MET675 2.3 27.1 1.0
O A:HOH1334 2.4 31.3 1.0
O A:HOH1306 2.5 40.0 1.0
C A:ASP672 3.3 27.9 1.0
C A:TYR669 3.4 29.5 1.0
C A:MET675 3.5 25.8 1.0
N A:LYS673 4.2 28.9 1.0
N A:MET675 4.2 29.2 1.0
CA A:LYS673 4.2 31.9 1.0
CA A:TYR669 4.3 25.7 1.0
CA A:ASP672 4.3 27.0 1.0
O A:LYS670 4.3 34.7 1.0
N A:SER676 4.3 24.3 1.0
CA A:SER676 4.4 22.7 1.0
C A:LYS673 4.4 31.4 1.0
CA A:MET675 4.4 27.0 1.0
N A:LYS670 4.4 30.4 1.0
N A:ASP672 4.4 30.1 1.0
CB A:ASP672 4.5 27.5 1.0
C A:LYS670 4.5 33.0 1.0
CA A:LYS670 4.6 33.7 1.0
O A:LYS673 4.6 32.8 1.0
CB A:TYR669 4.7 26.3 1.0
N A:GLN674 4.8 33.5 1.0
CB A:SER676 4.9 23.4 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 23:17:20 2025

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