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Potassium in PDB 7g7o: Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm, PDB code: 7g7o 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) 45.61 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.911, 91.222, 118.633, 90, 90, 90
R / Rfree (%) 18.7 / 23.9

Other elements in 7g7o:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm also contains other interesting chemical elements:

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

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm (pdb code 7g7o). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm, PDB code: 7g7o:

Potassium binding site 1 out of 1 in 7g7o

Go back to Potassium Binding Sites List in 7g7o
Potassium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 3-Methyl-5-[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]Azepine-2-Carbonyl]-1H- Benzimidazol-2-One, I.E. Smiles C1C[C@@H]2[C@H](CCN1C(=O)C1CC(Nc(C1) OCC1CCOCC1)C1CC1)Cn(C2)C(=O)C1CCC2C(C1)N(C(=O)N2)C with IC50=0.00527031 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K905

b:40.5
occ:1.00
 O A:HOH1230 2.2 47.2 1.0
O A:HOH1254 2.3 48.2 1.0
O A:ASP672 2.3 35.2 1.0
O A:TYR669 2.3 40.3 1.0
O A:HOH1145 2.4 37.4 1.0
O A:MET675 2.4 41.1 1.0
C A:ASP672 3.5 40.9 1.0
C A:TYR669 3.5 40.6 1.0
C A:MET675 3.5 42.9 1.0
N A:MET675 4.1 40.9 1.0
CA A:TYR669 4.3 34.0 1.0
O A:LYS670 4.3 42.3 1.0
CA A:LYS673 4.3 44.7 1.0
N A:LYS673 4.4 39.7 1.0
N A:SER676 4.4 39.1 1.0
CA A:MET675 4.4 42.1 1.0
C A:LYS673 4.4 43.8 1.0
CA A:SER676 4.4 34.0 1.0
CA A:ASP672 4.4 38.5 1.0
N A:LYS670 4.5 39.5 1.0
O A:LYS673 4.5 47.7 1.0
N A:ASP672 4.6 44.2 1.0
CA A:LYS670 4.6 44.9 1.0
CB A:ASP672 4.6 41.1 1.0
CB A:TYR669 4.7 31.4 1.0
C A:LYS670 4.7 41.1 1.0
N A:GLN674 4.9 51.0 1.0
CB A:SER676 4.9 32.7 1.0
C A:GLN674 5.0 52.3 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 20:08:05 2025

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