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Sodium in PDB 7g4q: Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm, PDB code: 7g4q 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) 48.82 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.95, 91.983, 120.009, 90, 90, 90
R / Rfree (%) 17.9 / 22.4

Other elements in 7g4q:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm (pdb code 7g4q). 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 (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm, PDB code: 7g4q:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g4q

Go back to Sodium Binding Sites List in 7g4q
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 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 (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:30.3
occ:1.00
 O A:SER804 2.2 23.0 1.0
OG A:SER807 2.3 26.3 1.0
O A:HOH1389 2.4 35.0 1.0
O A:HOH1326 2.5 36.1 1.0
O A:ASN801 2.5 22.8 1.0
O A:HOH1158 2.5 29.3 1.0
C A:SER804 3.3 23.9 1.0
C A:ASN801 3.4 22.7 1.0
CB A:SER807 3.4 23.7 1.0
CA A:ASP802 3.9 30.8 1.0
N A:SER807 4.0 27.2 1.0
N A:ASP802 4.0 26.5 1.0
O A:ASP802 4.1 27.6 1.0
N A:CYS805 4.1 29.6 1.0
CA A:CYS805 4.2 30.7 1.0
N A:SER804 4.2 22.6 1.0
C A:ASP802 4.2 30.9 1.0
CA A:SER804 4.3 21.5 1.0
CA A:SER807 4.3 31.8 1.0
O A:HOH1092 4.4 40.1 1.0
C A:CYS805 4.4 30.1 1.0
CB A:ASN801 4.4 23.4 1.0
CA A:ASN801 4.4 23.9 1.0
O A:CYS805 4.4 30.6 1.0
CB A:SER804 4.5 30.3 1.0
O A:HOH1167 4.6 38.2 1.0
OD1 A:ASP802 4.8 36.4 1.0
N A:ASN806 4.8 30.6 1.0
N A:GLU803 5.0 23.3 1.0

Sodium binding site 2 out of 2 in 7g4q

Go back to Sodium Binding Sites List in 7g4q
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 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 (3-Chloro-5- Cyanophenyl)Methyl Rac-(3AR,6AS)-2-(1H-Benzotriazole-5-Carbonyl)-1,3, 3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles C1N(C[C@@H]2[C@H]1CN(C2)C(=O)C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl) C#N with IC50=0.729656 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:47.8
occ:1.00
 OG1 A:THR567 2.3 41.0 1.0
O A:THR567 2.3 37.6 1.0
O A:HOH1364 2.4 38.8 1.0
O A:ASN650 2.4 33.7 1.0
O A:HOH1378 2.6 51.3 1.0
O A:HOH1375 2.7 54.0 1.0
C A:THR567 3.1 48.0 1.0
C A:ASN650 3.4 27.7 1.0
N A:THR567 3.4 37.5 1.0
CB A:THR567 3.4 49.3 1.0
CA A:THR567 3.5 46.7 1.0
CB A:ASN650 4.0 42.4 1.0
CA A:CYS651 4.1 33.1 1.0
N A:CYS651 4.1 27.2 1.0
N A:CYS568 4.2 39.4 1.0
CA A:ASN650 4.3 37.0 1.0
N A:VAL652 4.4 24.1 1.0
CG2 A:THR567 4.6 48.5 1.0
C A:CYS651 4.6 35.9 1.0
CA A:CYS568 4.6 42.4 1.0
C A:CYS566 4.7 41.6 1.0
O A:HOH1095 5.0 38.7 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 23:18:33 2025

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