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Sodium in PDB 7g70: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm, PDB code: 7g70 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) 46.02 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.438, 92.042, 120.427, 90, 90, 90
R / Rfree (%) 20.5 / 24

Other elements in 7g70:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm (pdb code 7g70). 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 [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm, PDB code: 7g70:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g70

Go back to Sodium Binding Sites List in 7g70
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 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 [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:37.9
occ:1.00
 O A:HOH1399 2.2 41.5 1.0
OG A:SER807 2.3 28.3 1.0
O A:SER804 2.5 26.2 1.0
O A:HOH1255 2.5 41.2 1.0
O A:HOH1126 2.5 36.9 1.0
O A:ASN801 2.6 22.9 1.0
CB A:SER807 3.4 27.1 1.0
C A:ASN801 3.5 23.1 1.0
C A:SER804 3.6 29.4 1.0
CA A:ASP802 3.9 28.3 1.0
N A:ASP802 4.0 26.0 1.0
N A:SER807 4.0 29.3 1.0
O A:HOH1045 4.1 36.4 1.0
O A:ASP802 4.2 26.4 1.0
C A:ASP802 4.3 27.1 1.0
CA A:SER807 4.3 30.2 1.0
CA A:CYS805 4.3 31.5 1.0
N A:CYS805 4.4 28.8 1.0
C A:CYS805 4.4 31.3 1.0
CB A:ASN801 4.4 24.2 1.0
O A:CYS805 4.5 31.7 1.0
N A:SER804 4.5 25.1 1.0
CA A:ASN801 4.5 23.8 1.0
CA A:SER804 4.6 25.5 1.0
O A:HOH1162 4.7 36.0 1.0
OD1 A:ASP802 4.8 34.3 1.0
O A:HOH1190 4.8 36.9 1.0
N A:ASN806 4.9 31.0 1.0
C A:SER807 4.9 32.7 1.0
CB A:SER804 5.0 29.0 1.0

Sodium binding site 2 out of 2 in 7g70

Go back to Sodium Binding Sites List in 7g70
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 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 [(3AS,6AS)-5-[2- (Dimethylamino)-6-(Oxan-4-Ylmethoxy)Pyridine-4-Carbonyl]-1,3,3A,4,6, 6A-Hexahydropyrrolo[3,4-C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl) Methanone, I.E. Smiles C1(CCC2C(C1)N=NN2)C(=O)N1C[C@@H]2[C@@H](C1) Cn(C2)C(=O)C1CC(Nc(C1)OCC1CCOCC1)N(C)C with IC50=0.0094279 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:19.3
occ:1.00
 O A:HOH1353 2.0 38.9 1.0
O A:ASP672 2.2 29.4 1.0
O A:TYR669 2.3 29.5 1.0
O A:MET675 2.3 27.4 1.0
O A:HOH1392 2.3 33.0 1.0
O A:HOH1316 2.4 28.9 1.0
C A:MET675 3.4 25.3 1.0
C A:TYR669 3.4 31.3 1.0
C A:ASP672 3.4 32.4 1.0
N A:MET675 4.2 28.3 1.0
CA A:TYR669 4.2 28.4 1.0
N A:SER676 4.3 22.1 1.0
CA A:SER676 4.3 22.9 1.0
CA A:MET675 4.3 25.3 1.0
O A:LYS670 4.4 37.8 1.0
N A:LYS673 4.4 33.1 1.0
CA A:ASP672 4.4 33.6 1.0
CA A:LYS673 4.4 36.5 1.0
N A:LYS670 4.4 30.9 1.0
C A:LYS673 4.5 35.5 1.0
CB A:ASP672 4.6 33.1 1.0
N A:ASP672 4.6 35.9 1.0
CB A:TYR669 4.6 26.3 1.0
CA A:LYS670 4.6 33.6 1.0
C A:LYS670 4.7 33.5 1.0
O A:LYS673 4.7 30.6 1.0
N A:GLN674 4.8 31.0 1.0
CB A:SER676 4.8 21.0 1.0
C A:GLN674 5.0 30.2 1.0
CB A:MET675 5.0 25.1 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 23:32:55 2025

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