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Sodium in PDB 7g6a: Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm, PDB code: 7g6a 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) 45.67 / 1.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.657, 91.334, 118.662, 90, 90, 90
R / Rfree (%) 19.2 / 22

Other elements in 7g6a:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms
Fluorine (F) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm (pdb code 7g6a). 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 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm, PDB code: 7g6a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6a

Go back to Sodium Binding Sites List in 7g6a
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 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 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:21.2
occ:1.00
 O A:HOH1353 2.3 21.0 1.0
O A:HOH1373 2.4 23.2 1.0
O A:SER804 2.4 17.3 1.0
OG A:SER807 2.4 18.3 1.0
O A:HOH1425 2.4 27.2 1.0
O A:ASN801 2.4 17.0 1.0
C A:ASN801 3.3 17.6 1.0
C A:SER804 3.4 17.3 1.0
CB A:SER807 3.5 19.3 1.0
CA A:ASP802 3.8 17.7 1.0
N A:ASP802 3.9 16.9 1.0
N A:SER807 4.1 20.5 1.0
C A:ASP802 4.2 16.8 1.0
O A:ASP802 4.2 16.0 1.0
CA A:CYS805 4.2 20.1 1.0
N A:CYS805 4.3 18.4 1.0
CB A:ASN801 4.3 17.2 1.0
CA A:SER807 4.3 21.2 1.0
O A:HOH1051 4.3 35.8 1.0
N A:SER804 4.3 16.1 1.0
C A:CYS805 4.4 20.9 1.0
CA A:SER804 4.4 15.6 1.0
CA A:ASN801 4.4 17.5 1.0
O A:CYS805 4.5 21.6 1.0
O A:HOH1094 4.7 28.7 1.0
CB A:SER804 4.7 16.2 1.0
OD1 A:ASP802 4.7 25.4 1.0
O A:HOH1306 4.7 27.8 1.0
N A:ASN806 4.9 20.5 1.0
N A:GLU803 4.9 14.9 1.0

Sodium binding site 2 out of 2 in 7g6a

Go back to Sodium Binding Sites List in 7g6a
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 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 5-(1-Acetyl-4- Piperidyl)-4-[(E)-[3,5-Bis(Trifluoromethyl)Phenyl]Azo]-1,2- Dihydropyrazol-3-One, I.E. Smiles Cc(=O)N1CCC(CC1) C2=C(\N=N\C3CC(Cc(C3)C(F)(F)F)C(F)(F)F)C(=O)NN2 with IC50=2.9986 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:22.4
occ:1.00
 O A:TYR669 2.3 23.6 1.0
O A:MET675 2.3 20.0 1.0
O A:ASP672 2.3 21.9 1.0
O A:HOH1387 2.4 30.2 1.0
O A:HOH1429 2.5 42.5 1.0
C A:TYR669 3.4 22.7 1.0
C A:MET675 3.5 19.2 1.0
C A:ASP672 3.5 22.6 1.0
N A:MET675 4.0 19.6 1.0
CA A:TYR669 4.2 19.8 1.0
CA A:MET675 4.3 18.6 1.0
CA A:LYS673 4.3 25.9 1.0
O A:LYS670 4.3 27.5 1.0
N A:SER676 4.4 16.6 1.0
N A:LYS673 4.4 22.2 1.0
CA A:ASP672 4.4 22.1 1.0
N A:ASP672 4.4 23.2 1.0
CA A:SER676 4.4 16.3 1.0
N A:LYS670 4.5 22.8 1.0
C A:LYS673 4.5 25.2 1.0
C A:LYS670 4.6 24.5 1.0
CA A:LYS670 4.6 26.2 1.0
CB A:TYR669 4.6 19.1 1.0
CB A:ASP672 4.6 21.9 1.0
O A:LYS673 4.6 25.3 1.0
N A:GLN674 4.9 23.2 1.0
CB A:MET675 4.9 18.1 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 23:25:46 2025

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