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Calcium in PDB 7g58: Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm, PDB code: 7g58 was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.97 / 1.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.319, 91.93, 119.742, 90, 90, 90
R / Rfree (%) 18.2 / 23.1

Other elements in 7g58:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm (pdb code 7g58). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm, PDB code: 7g58:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g58

Go back to Calcium Binding Sites List in 7g58
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:40.5
occ:1.00
 O A:HOH1363 2.2 43.4 1.0
O A:ASP672 2.2 33.1 1.0
O A:MET675 2.3 34.6 1.0
O A:TYR669 2.3 38.3 1.0
O A:HOH1323 2.5 34.8 1.0
O A:HOH1391 2.7 38.6 1.0
C A:MET675 3.4 30.3 1.0
C A:ASP672 3.4 41.4 1.0
C A:TYR669 3.5 39.0 1.0
N A:MET675 4.1 33.0 1.0
N A:SER676 4.2 27.8 1.0
CA A:TYR669 4.2 36.7 1.0
CA A:SER676 4.3 29.0 1.0
CA A:MET675 4.3 32.9 1.0
O A:LYS670 4.3 46.0 1.0
N A:LYS673 4.4 39.9 1.0
CA A:ASP672 4.4 32.6 1.0
CA A:LYS673 4.4 42.0 1.0
N A:LYS670 4.4 38.2 1.0
C A:LYS673 4.5 39.6 1.0
CB A:ASP672 4.6 35.1 1.0
N A:ASP672 4.6 42.4 1.0
O A:LYS673 4.6 36.7 1.0
CA A:LYS670 4.6 38.7 1.0
C A:LYS670 4.7 34.8 1.0
CB A:TYR669 4.7 36.5 1.0
CB A:SER676 4.8 29.9 1.0
N A:GLN674 4.9 37.3 1.0
C A:GLN674 4.9 39.0 1.0

Calcium binding site 2 out of 2 in 7g58

Go back to Calcium Binding Sites List in 7g58
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 2-[(3,3-Dimethyl-6- Propan-2-Yl-1,2-Dihydroinden-5-Yl)Oxy]-1-[Rac-(3AR,8AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4- D]Azepin-6-Yl]Ethanone, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2) C(=O)C1CC2C(CC1)Nn=N2)C(=O)COC1C(CC2C(C1)C(CC2)(C)C)C(C)C with IC50=0.00121852 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:24.9
occ:1.00
 O A:HOH1340 2.3 31.2 1.0
OD1 A:ASP743 2.3 26.8 1.0
OD1 A:ASP747 2.3 21.5 1.0
OD1 A:ASP739 2.3 24.0 1.0
O A:LEU745 2.4 21.5 1.0
OD1 A:ASN741 2.4 29.4 1.0
CG A:ASP743 3.3 25.3 1.0
CG A:ASN741 3.4 31.4 1.0
CG A:ASP739 3.5 22.1 1.0
C A:LEU745 3.5 26.7 1.0
CG A:ASP747 3.6 21.9 1.0
OD2 A:ASP743 3.8 30.8 1.0
ND2 A:ASN741 3.8 30.8 1.0
CA A:ASP739 3.9 24.4 1.0
N A:ASP747 3.9 24.0 1.0
C A:ARG746 4.0 25.0 1.0
N A:LEU745 4.1 22.8 1.0
O A:ARG746 4.1 22.7 1.0
CA A:ASP747 4.2 23.2 1.0
CB A:ASP739 4.2 24.0 1.0
CA A:LEU745 4.3 23.6 1.0
N A:ASP743 4.3 24.2 1.0
O A:PHE738 4.4 24.1 1.0
CB A:ASP747 4.4 22.9 1.0
N A:ASN741 4.4 24.8 1.0
C A:ASP739 4.4 26.0 1.0
OD2 A:ASP739 4.4 25.1 1.0
CB A:ASP743 4.5 25.4 1.0
OD2 A:ASP747 4.5 26.0 1.0
N A:ARG746 4.5 22.9 1.0
CB A:LEU745 4.5 27.2 1.0
OE2 A:GLU751 4.7 38.2 1.0
N A:TYR740 4.7 28.1 1.0
CA A:ARG746 4.7 22.6 1.0
CB A:ASN741 4.7 25.8 1.0
N A:TYR742 4.8 25.6 1.0
CA A:ASP743 4.8 26.1 1.0
C A:ASN741 4.9 30.4 1.0
N A:GLY744 4.9 24.7 1.0
CA A:ASN741 4.9 25.8 1.0
O A:HOH1372 5.0 42.4 1.0
O A:ASP739 5.0 26.0 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 15:49:18 2025

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