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Sodium in PDB 7g7f: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm, PDB code: 7g7f 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) 48.69 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.009, 91.379, 119.499, 90, 90, 90
R / Rfree (%) 18.7 / 23.1

Other elements in 7g7f:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Potassium (K) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm (pdb code 7g7f). 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 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm, PDB code: 7g7f:

Sodium binding site 1 out of 1 in 7g7f

Go back to Sodium Binding Sites List in 7g7f
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 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 1H-Benzotriazol-5- Yl-[Rac-(3AR,8AS)-6-[2-Cyclopropyl-6-(Oxan-4-Ylmethoxy)Pyridine-4- Carbonyl]-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepin-2- Yl]Methanone, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N=NN2 with IC50=0.00129469 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:46.3
occ:1.00
 OG A:SER807 2.3 34.7 1.0
O A:HOH1247 2.4 42.2 1.0
O A:HOH1314 2.4 48.2 1.0
O A:HOH1220 2.4 39.6 1.0
O A:SER804 2.5 32.6 1.0
O A:ASN801 2.7 29.0 1.0
C A:ASN801 3.5 33.3 1.0
CB A:SER807 3.5 36.8 1.0
C A:SER804 3.6 35.5 1.0
CA A:ASP802 3.9 37.0 1.0
N A:ASP802 4.1 33.6 1.0
N A:SER807 4.1 41.6 1.0
O A:ASP802 4.2 35.8 1.0
C A:ASP802 4.3 38.8 1.0
CA A:CYS805 4.3 38.9 1.0
CA A:SER807 4.3 40.1 1.0
N A:CYS805 4.4 35.5 1.0
C A:CYS805 4.4 42.0 1.0
O A:CYS805 4.4 42.5 1.0
O A:HOH1039 4.5 45.3 1.0
N A:SER804 4.5 33.0 1.0
CB A:ASN801 4.5 31.6 1.0
CA A:ASN801 4.6 33.1 1.0
CA A:SER804 4.6 30.2 1.0
OD1 A:ASP802 4.7 42.2 1.0
O A:HOH1137 4.8 44.3 1.0
N A:ASN806 4.9 42.4 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 23:32:56 2025

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