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Calcium in PDB 7g3z: Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm, PDB code: 7g3z was solved by M.Stihle, J.Benz, D.Hunziker, L.Hu, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.01 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.107, 92.02, 119.812, 90, 90, 90
R / Rfree (%) 19.1 / 23.1

Other elements in 7g3z:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm also contains other interesting chemical elements:

Fluorine (F) 1 atom
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 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm (pdb code 7g3z). 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 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm, PDB code: 7g3z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3z

Go back to Calcium Binding Sites List in 7g3z
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 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 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:25.0
occ:1.00
 OD1 A:ASP743 2.3 26.1 1.0
OD1 A:ASP747 2.3 26.0 1.0
OD1 A:ASP739 2.3 23.4 1.0
OD1 A:ASN741 2.3 27.0 1.0
O A:HOH1341 2.4 29.6 1.0
O A:LEU745 2.4 23.2 1.0
CG A:ASP743 3.2 27.0 1.0
CG A:ASN741 3.4 28.7 1.0
CG A:ASP739 3.5 22.1 1.0
C A:LEU745 3.5 22.3 1.0
CG A:ASP747 3.6 26.3 1.0
OD2 A:ASP743 3.6 29.8 1.0
ND2 A:ASN741 3.9 27.4 1.0
CA A:ASP739 3.9 23.3 1.0
N A:ASP747 4.0 22.7 1.0
N A:LEU745 4.1 22.1 1.0
C A:ARG746 4.1 24.9 1.0
CB A:ASP739 4.1 21.0 1.0
O A:ARG746 4.2 24.4 1.0
CA A:LEU745 4.2 22.6 1.0
CA A:ASP747 4.2 25.1 1.0
N A:ASP743 4.2 24.1 1.0
OD2 A:ASP747 4.4 25.5 1.0
OD2 A:ASP739 4.4 22.1 1.0
C A:ASP739 4.4 22.8 1.0
N A:ASN741 4.5 25.8 1.0
CB A:ASP743 4.5 24.4 1.0
CB A:LEU745 4.5 25.2 1.0
O A:PHE738 4.5 21.3 1.0
N A:ARG746 4.5 22.7 1.0
CB A:ASP747 4.5 24.1 1.0
N A:TYR740 4.7 22.9 1.0
OE2 A:GLU751 4.7 42.9 1.0
N A:TYR742 4.7 24.9 1.0
CB A:ASN741 4.7 27.7 1.0
O A:HOH1284 4.7 49.1 1.0
CA A:ASP743 4.8 24.6 1.0
CA A:ARG746 4.8 22.9 1.0
C A:ASN741 4.8 27.9 1.0
N A:GLY744 4.8 24.2 1.0
CA A:ASN741 4.9 26.7 1.0

Calcium binding site 2 out of 2 in 7g3z

Go back to Calcium Binding Sites List in 7g3z
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 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 3-(2-Fluoro-4- Methylphenyl)-N-[(5-Methylpyrazin-2-Yl)Methyl]-5-(5-Propyltetrazol-1- Yl)Benzamide, I.E. Smiles C(C1NCC(NC1)C)Nc(=O)C1CC(Cc(N2C(=Nn=N2) Ccc)C1)C1CCC(CC1F)C with IC50=0.771863 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:34.3
occ:1.00
 OXT A:ACT901 2.1 34.0 1.0
O A:HOH1313 2.2 41.3 1.0
O A:ASP672 2.3 34.6 1.0
O A:TYR669 2.3 34.6 1.0
O A:MET675 2.3 32.4 1.0
O A:HOH1351 2.4 35.3 1.0
C A:ACT901 3.4 35.9 1.0
C A:MET675 3.4 30.9 1.0
C A:ASP672 3.5 38.2 1.0
C A:TYR669 3.5 36.5 1.0
N A:MET675 4.1 34.6 1.0
O A:ACT901 4.2 42.6 1.0
CA A:TYR669 4.2 32.5 1.0
CH3 A:ACT901 4.2 31.9 1.0
N A:SER676 4.3 26.8 1.0
CA A:LYS673 4.3 39.7 1.0
N A:LYS673 4.3 38.9 1.0
CA A:SER676 4.3 27.5 1.0
CA A:MET675 4.4 31.4 1.0
O A:LYS670 4.4 40.9 1.0
C A:LYS673 4.4 39.6 1.0
CA A:ASP672 4.4 34.4 1.0
N A:LYS670 4.5 36.9 1.0
O A:LYS673 4.5 37.1 1.0
N A:ASP672 4.6 41.2 1.0
CB A:ASP672 4.6 34.7 1.0
CB A:TYR669 4.6 31.2 1.0
CA A:LYS670 4.6 41.2 1.0
C A:LYS670 4.7 39.5 1.0
N A:GLN674 4.9 39.6 1.0
C A:GLN674 4.9 41.3 1.0
CB A:SER676 4.9 27.5 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: Wed Jul 9 22:23:21 2025

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