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Sodium in PDB 7g4n: Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm, PDB code: 7g4n 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) 45.74 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.726, 91.477, 118.973, 90, 90, 90
R / Rfree (%) 18 / 21.5

Other elements in 7g4n:

The structure of Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 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-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm (pdb code 7g4n). 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-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm, PDB code: 7g4n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g4n

Go back to Sodium Binding Sites List in 7g4n
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:21.1
occ:1.00
 OG A:SER807 2.2 22.5 1.0
O A:SER804 2.4 20.0 1.0
O A:HOH1315 2.4 24.8 1.0
O A:HOH1451 2.4 26.8 1.0
O A:HOH1410 2.4 25.3 1.0
O A:ASN801 2.5 17.9 1.0
C A:ASN801 3.3 18.9 1.0
CB A:SER807 3.4 22.6 1.0
C A:SER804 3.5 20.4 1.0
CA A:ASP802 3.9 19.8 1.0
N A:ASP802 4.0 19.3 1.0
N A:SER807 4.0 20.8 1.0
O A:HOH1496 4.1 38.7 1.0
O A:HOH1034 4.2 32.0 1.0
C A:ASP802 4.2 20.0 1.0
CA A:SER807 4.2 22.8 1.0
O A:ASP802 4.2 19.8 1.0
CB A:ASN801 4.3 18.3 1.0
CA A:CYS805 4.3 21.4 1.0
N A:CYS805 4.3 20.2 1.0
N A:SER804 4.3 18.0 1.0
CA A:SER804 4.4 17.3 1.0
CA A:ASN801 4.4 18.9 1.0
C A:CYS805 4.4 22.6 1.0
O A:CYS805 4.5 24.2 1.0
CB A:SER804 4.6 18.3 1.0
O A:HOH1117 4.6 32.5 1.0
OD1 A:ASP802 4.8 26.8 1.0
O A:HOH1295 4.9 31.7 1.0
N A:ASN806 4.9 22.6 1.0
C A:SER807 5.0 24.7 1.0

Sodium binding site 2 out of 2 in 7g4n

Go back to Sodium Binding Sites List in 7g4n
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [4- (Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 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-(6-Sulfamoylpyridine-3- Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4-C]Pyrrole-5-Carboxylate, I.E. Smiles Fc(OC1CCC(CC1)Coc(=O)N1C[C@H]2[C@H](C1)Cn(C2)C(=O) C1CNC(CC1)S(=O)(=O)N)(F)F with IC50=0.0134798 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:22.9
occ:1.00
 O A:TYR669 2.2 25.3 1.0
O A:ASP672 2.3 23.7 1.0
O A:MET675 2.3 23.3 1.0
O A:HOH1309 2.4 29.7 1.0
O A:HOH1440 2.6 40.5 1.0
O A:HOH1423 2.8 42.1 1.0
C A:TYR669 3.4 25.5 1.0
C A:MET675 3.5 21.8 1.0
C A:ASP672 3.5 24.9 1.0
N A:MET675 4.1 21.5 1.0
CA A:TYR669 4.2 22.2 1.0
O A:LYS670 4.3 29.2 1.0
CA A:MET675 4.3 20.9 1.0
CA A:LYS673 4.4 27.4 1.0
N A:LYS670 4.4 26.4 1.0
CA A:ASP672 4.4 24.7 1.0
N A:SER676 4.4 17.3 1.0
N A:ASP672 4.4 24.0 1.0
N A:LYS673 4.4 24.9 1.0
CA A:SER676 4.5 20.0 1.0
C A:LYS673 4.5 25.8 1.0
CA A:LYS670 4.6 30.0 1.0
C A:LYS670 4.6 27.9 1.0
CB A:TYR669 4.6 20.2 1.0
CB A:ASP672 4.6 24.1 1.0
O A:HOH1495 4.6 37.5 1.0
O A:LYS673 4.6 28.7 1.0
CB A:MET675 4.9 19.5 1.0
N A:GLN674 4.9 24.7 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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