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Calcium in PDB 7g3b: Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm, PDB code: 7g3b was solved by M.Stihle, J.Benz, D.Hunziker, H.Richter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.88 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.149, 91.841, 119.912, 90, 90, 90
R / Rfree (%) 18.2 / 21.3

Other elements in 7g3b:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm (pdb code 7g3b). 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-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm, PDB code: 7g3b:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3b

Go back to Calcium Binding Sites List in 7g3b
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 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-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:19.8
occ:1.00
 OD1 A:ASP171 1.8 19.6 0.7
OG1 A:THR209 1.9 17.4 1.0
NE2 A:HIS359 2.0 14.2 1.0
OD1 A:ASP171 2.1 11.8 0.3
OD2 A:ASP358 2.2 18.6 1.0
CG A:ASP171 2.6 11.8 0.3
OD2 A:ASP171 2.6 11.4 0.3
CG A:ASP171 2.8 19.7 0.7
CE1 A:HIS359 2.9 12.8 1.0
CB A:THR209 2.9 15.6 1.0
CG A:ASP358 3.1 15.3 1.0
CD2 A:HIS359 3.1 13.6 1.0
CG2 A:THR209 3.2 18.2 1.0
OD2 A:ASP171 3.3 23.8 0.7
CA A:THR209 3.4 14.3 1.0
OD1 A:ASP358 3.4 14.9 1.0
O A:HOH1171 3.9 35.2 1.0
N A:THR209 3.9 12.4 1.0
CB A:ASP171 3.9 12.3 0.3
ND1 A:HIS359 4.0 13.4 1.0
CB A:ASP171 4.0 16.1 0.7
OD2 A:ASP311 4.1 20.0 1.0
CG A:HIS359 4.1 13.0 1.0
O1 A:SO4904 4.1 28.9 1.0
N A:GLY172 4.2 14.0 1.0
CA A:ASP171 4.3 15.0 0.7
O3 A:SO4904 4.3 31.9 1.0
CB A:ASP358 4.3 13.5 1.0
CA A:ASP171 4.3 13.6 0.3
CE1 A:HIS474 4.4 15.4 1.0
CG A:ASP311 4.5 17.4 1.0
ZN A:ZN906 4.5 16.5 1.0
C A:ASP171 4.6 14.7 1.0
NE2 A:HIS474 4.6 15.3 1.0
C A:THR209 4.7 15.8 1.0
C A:LYS208 4.7 13.7 1.0
S A:SO4904 4.7 47.2 1.0
CB A:ASP311 4.9 14.9 1.0
OD1 A:ASP311 5.0 19.8 1.0
CA A:GLY172 5.0 13.6 1.0

Calcium binding site 2 out of 2 in 7g3b

Go back to Calcium Binding Sites List in 7g3b
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 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-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:14.0
occ:1.00
 OD1 A:ASN741 2.3 16.2 1.0
O A:LEU745 2.3 13.5 1.0
OD1 A:ASP747 2.3 15.2 1.0
O A:HOH1410 2.3 17.8 1.0
OD1 A:ASP739 2.4 13.2 1.0
OD1 A:ASP743 2.4 16.0 1.0
CG A:ASP743 3.3 17.7 1.0
CG A:ASN741 3.4 18.4 1.0
C A:LEU745 3.5 13.7 1.0
CG A:ASP739 3.5 13.2 1.0
CG A:ASP747 3.5 14.7 1.0
OD2 A:ASP743 3.7 20.0 1.0
ND2 A:ASN741 3.9 20.1 1.0
CA A:ASP739 4.0 11.9 1.0
N A:ASP747 4.0 14.5 1.0
C A:ARG746 4.0 14.0 1.0
N A:LEU745 4.0 13.3 1.0
CA A:ASP747 4.1 14.2 1.0
CA A:LEU745 4.2 14.0 1.0
O A:ARG746 4.2 15.2 1.0
CB A:ASP739 4.2 13.3 1.0
N A:ASP743 4.3 14.9 1.0
OD2 A:ASP739 4.4 13.0 1.0
CB A:LEU745 4.4 14.5 1.0
CB A:ASP747 4.4 14.2 1.0
OD2 A:ASP747 4.5 16.1 1.0
N A:ASN741 4.5 13.7 1.0
N A:ARG746 4.5 14.5 1.0
C A:ASP739 4.5 13.5 1.0
O A:PHE738 4.5 13.4 1.0
CB A:ASP743 4.6 15.6 1.0
O A:HOH1326 4.6 27.2 1.0
OE2 A:GLU751 4.6 25.3 1.0
CA A:ARG746 4.7 13.4 1.0
CB A:ASN741 4.7 16.8 1.0
N A:TYR740 4.7 12.7 1.0
N A:TYR742 4.8 13.8 1.0
CA A:ASP743 4.8 14.5 1.0
N A:GLY744 4.9 13.4 1.0
C A:ASN741 4.9 15.1 1.0
CA A:ASN741 4.9 15.1 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 15:37:04 2025

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