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Sodium in PDB 7g3i: Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm, PDB code: 7g3i was solved by M.Stihle, J.Benz, D.Hunziker, E.Pinard, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.81 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.988, 91.306, 118.107, 90, 90, 90
R / Rfree (%) 17.2 / 21.2

Other elements in 7g3i:

The structure of Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm (pdb code 7g3i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm, PDB code: 7g3i:

Sodium binding site 1 out of 1 in 7g3i

Go back to Sodium Binding Sites List in 7g3i
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 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 (6-Methylsulfonyl- 1,6-Diazaspiro[3.3]Heptan-1-Yl)-[2-[[3-Propan-2-Yl-5- (Trifluoromethoxy)Phenyl]Methylamino]Pyrimidin-5-Yl]Methanone, I.E. Smiles Cc(C)C1CC(Cc(C1)Oc(F)(F)F)CNC1NCC(CN1)C(=O)N1CCC21CN(C2)S(=O) (=O)C with IC50=0.018213 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:30.5
occ:1.00
 OG A:SER807 2.3 25.2 1.0
O A:SER804 2.4 22.9 1.0
O A:HOH1287 2.4 31.0 1.0
O A:HOH1071 2.6 29.2 1.0
O A:HOH1411 2.6 30.3 1.0
O A:ASN801 2.6 19.9 1.0
C A:ASN801 3.4 22.1 1.0
CB A:SER807 3.4 27.4 1.0
C A:SER804 3.5 24.0 1.0
CA A:ASP802 3.9 24.0 1.0
N A:ASP802 4.0 22.3 1.0
N A:SER807 4.1 28.7 1.0
O A:HOH1088 4.2 34.3 1.0
N A:CYS805 4.3 25.0 1.0
CA A:CYS805 4.3 29.1 1.0
CA A:SER807 4.3 28.9 1.0
C A:ASP802 4.3 24.5 1.0
O A:ASP802 4.3 22.7 1.0
CB A:ASN801 4.3 25.4 1.0
C A:CYS805 4.4 30.3 1.0
O A:CYS805 4.4 31.6 1.0
CA A:ASN801 4.4 23.7 1.0
N A:SER804 4.5 23.4 1.0
CA A:SER804 4.5 23.3 1.0
OD1 A:ASP802 4.5 28.0 1.0
O A:HOH1150 4.6 38.9 1.0
O A:HOH1333 4.7 34.1 1.0
CB A:SER804 4.8 23.9 1.0
C A:SER807 5.0 34.7 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 23:12:39 2025

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