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Sodium in PDB 7g5r: Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r 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) 48.89 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.288, 91.722, 120.027, 90, 90, 90
R / Rfree (%) 20 / 25

Other elements in 7g5r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm (pdb code 7g5r). 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm, PDB code: 7g5r:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g5r

Go back to Sodium Binding Sites List in 7g5r
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:34.4
occ:1.00
 OG A:SER807 2.2 33.1 1.0
O A:HOH1236 2.3 36.7 1.0
O A:HOH1384 2.4 39.0 1.0
O A:HOH1190 2.4 30.8 1.0
O A:SER804 2.4 34.3 1.0
O A:ASN801 2.8 31.5 1.0
CB A:SER807 3.4 33.8 1.0
C A:SER804 3.5 34.1 1.0
C A:ASN801 3.6 29.9 1.0
CA A:ASP802 3.9 29.9 1.0
N A:SER807 3.9 39.5 1.0
N A:ASP802 4.1 29.5 1.0
CA A:CYS805 4.2 36.7 1.0
O A:ASP802 4.2 30.2 1.0
CA A:SER807 4.2 36.9 1.0
C A:ASP802 4.3 30.0 1.0
N A:CYS805 4.3 34.0 1.0
C A:CYS805 4.3 40.7 1.0
O A:CYS805 4.5 39.4 1.0
N A:SER804 4.5 30.4 1.0
CB A:ASN801 4.5 27.9 1.0
CA A:SER804 4.5 31.0 1.0
CA A:ASN801 4.6 30.4 1.0
O A:HOH1107 4.6 38.9 1.0
N A:ASN806 4.7 42.4 1.0
OD1 A:ASP802 4.8 29.2 1.0
C A:SER807 4.9 37.3 1.0
CB A:SER804 5.0 32.7 1.0
O A:HOH1180 5.0 29.8 1.0

Sodium binding site 2 out of 2 in 7g5r

Go back to Sodium Binding Sites List in 7g5r
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 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 1H-Benzotriazol-5- Yl-[Rac-(1R,2R,6S,7S)-9-[5-Cyclopropyl-6-(2,2,2-Trifluoroethoxy) Pyridine-3-Carbonyl]-4,9-Diazatricyclo[5.3.0.02,6]Decan-4- Yl]Methanone, I.E. Smiles N1(C[C@H]2[C@@H](C1)[C@H]1[C@@H]2CN(C1) C(=O)C1CCC2C(C1)N=NN2)C(=O)C1CC(C(NC1)Occ(F)(F)F)C1CC1 with IC50=0.00395687 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:24.7
occ:1.00
 O A:HOH1348 2.1 42.7 1.0
O A:ASP672 2.2 38.9 1.0
O A:TYR669 2.3 37.6 1.0
O A:MET675 2.3 33.0 1.0
O A:HOH1367 2.3 41.6 1.0
O A:HOH1405 2.9 42.3 1.0
C A:MET675 3.4 32.1 1.0
C A:ASP672 3.5 38.8 1.0
C A:TYR669 3.5 38.4 1.0
N A:SER676 4.1 31.0 1.0
N A:MET675 4.1 35.6 1.0
CA A:SER676 4.2 31.8 1.0
CA A:TYR669 4.3 36.2 1.0
CA A:MET675 4.3 32.5 1.0
O A:LYS670 4.3 41.2 1.0
N A:LYS673 4.4 37.7 1.0
CA A:ASP672 4.4 39.4 1.0
CA A:LYS673 4.4 40.2 1.0
N A:LYS670 4.4 39.4 1.0
C A:LYS673 4.5 38.3 1.0
O A:LYS673 4.5 34.0 1.0
CB A:ASP672 4.6 37.1 1.0
N A:ASP672 4.6 41.4 1.0
CA A:LYS670 4.6 41.9 1.0
C A:LYS670 4.6 41.8 1.0
CB A:TYR669 4.7 37.3 1.0
CB A:SER676 4.8 30.5 1.0
N A:GLN674 4.9 37.2 1.0
C A:GLN674 5.0 39.9 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 23:22:55 2025

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