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Sodium in PDB 7g48: Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm, PDB code: 7g48 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) 46.10 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.307, 92.204, 119.901, 90, 90, 90
R / Rfree (%) 18.6 / 22.1

Other elements in 7g48:

The structure of Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm (pdb code 7g48). 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-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm, PDB code: 7g48:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g48

Go back to Sodium Binding Sites List in 7g48
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 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-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:30.4
occ:1.00
 O A:SER804 2.3 22.3 1.0
O A:HOH1449 2.3 33.1 1.0
OG A:SER807 2.4 24.2 1.0
O A:ASN801 2.5 20.6 1.0
O A:HOH1302 2.6 34.0 1.0
O A:HOH1207 2.6 32.5 1.0
C A:ASN801 3.4 20.4 1.0
C A:SER804 3.4 23.0 1.0
CB A:SER807 3.5 23.8 1.0
CA A:ASP802 3.9 24.0 1.0
N A:ASP802 4.0 21.0 1.0
N A:SER807 4.0 27.5 1.0
CA A:CYS805 4.1 26.0 1.0
N A:CYS805 4.2 22.6 1.0
O A:ASP802 4.2 21.8 1.0
C A:ASP802 4.2 23.3 1.0
C A:CYS805 4.3 27.4 1.0
O A:HOH1111 4.3 32.4 1.0
CA A:SER807 4.3 26.7 1.0
N A:SER804 4.3 20.5 1.0
O A:CYS805 4.3 26.8 1.0
CA A:SER804 4.4 20.0 1.0
CB A:ASN801 4.4 20.3 1.0
CA A:ASN801 4.5 20.1 1.0
O A:HOH1187 4.7 32.9 1.0
CB A:SER804 4.7 21.1 1.0
OD1 A:ASP802 4.7 28.4 1.0
N A:ASN806 4.8 26.0 1.0
O A:HOH1183 4.9 34.6 1.0

Sodium binding site 2 out of 2 in 7g48

Go back to Sodium Binding Sites List in 7g48
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [(3AS,6AS)-5-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 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-(4- Methoxynaphthalene-2-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrol-2-Yl]-(1H-Benzotriazol-5-Yl)Methanone, I.E. Smiles N1(C[C@@H]2[C@@H](C1)Cn(C2)C(=O)C1CC(C2C(C1)CCCC2)Oc)C(=O) C1CCC2C(C1)N=NN2 with IC50=0.11329 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:30.9
occ:1.00
 O A:MET675 2.3 25.3 1.0
O A:TYR669 2.3 29.1 1.0
O A:ASP672 2.4 28.3 1.0
O A:HOH1410 2.5 31.4 1.0
C A:MET675 3.4 24.8 1.0
C A:TYR669 3.5 30.0 1.0
C A:ASP672 3.6 28.7 1.0
N A:MET675 4.1 27.2 1.0
CA A:TYR669 4.2 27.2 1.0
CA A:MET675 4.3 25.1 1.0
N A:SER676 4.3 22.1 1.0
CA A:LYS673 4.3 31.3 1.0
O A:LYS670 4.4 31.8 1.0
CA A:SER676 4.4 22.0 1.0
N A:LYS673 4.4 29.8 1.0
C A:LYS673 4.5 32.1 1.0
O A:HOH1485 4.5 38.6 1.0
N A:LYS670 4.5 27.8 1.0
CA A:ASP672 4.6 28.4 1.0
CB A:TYR669 4.6 26.4 1.0
N A:ASP672 4.6 30.0 1.0
C A:LYS670 4.6 29.4 1.0
O A:LYS673 4.6 29.5 1.0
CA A:LYS670 4.7 31.1 1.0
CB A:ASP672 4.7 28.3 1.0
N A:GLN674 4.9 29.7 1.0
CB A:MET675 4.9 24.5 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 23:17:20 2025

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