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Calcium in PDB 7g6i: Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm, PDB code: 7g6i was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.02, 91.688, 120.003, 90, 90, 90
R / Rfree (%) 18.9 / 23.2

Other elements in 7g6i:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm (pdb code 7g6i). 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 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm, PDB code: 7g6i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6i

Go back to Calcium Binding Sites List in 7g6i
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 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 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:55.7
occ:1.00
 OG1 A:THR209 1.8 24.1 1.0
OD1 A:ASP171 1.8 31.0 1.0
NE2 A:HIS359 2.1 22.6 1.0
OD2 A:ASP358 2.5 26.1 1.0
CG A:ASP171 2.8 30.3 1.0
CE1 A:HIS359 2.9 21.6 1.0
CB A:THR209 2.9 23.1 1.0
CD2 A:HIS359 3.2 21.6 1.0
OD2 A:ASP171 3.2 37.2 1.0
CG A:ASP358 3.3 23.7 1.0
CG2 A:THR209 3.3 24.2 1.0
O A:HOH1074 3.4 38.6 1.0
CA A:THR209 3.4 22.7 1.0
OD1 A:ASP358 3.5 21.9 1.0
N A:THR209 3.9 22.6 1.0
ND1 A:HIS359 4.0 21.7 1.0
OD1 A:ASP311 4.0 24.8 1.0
CB A:ASP171 4.1 25.6 1.0
CG A:HIS359 4.2 21.8 1.0
CE1 A:HIS474 4.2 21.8 1.0
N A:GLY172 4.2 23.3 1.0
CG A:ASP311 4.3 25.3 1.0
CA A:ASP171 4.4 25.0 1.0
ZN A:ZN904 4.4 26.5 1.0
NE2 A:HIS474 4.4 22.3 1.0
O A:HOH1001 4.6 25.8 1.0
CB A:ASP358 4.6 21.4 1.0
C A:ASP171 4.6 23.5 1.0
OD2 A:ASP311 4.7 27.4 1.0
O A:HOH1450 4.7 33.9 1.0
C A:LYS208 4.7 23.5 1.0
CB A:ASP311 4.7 25.0 1.0
C A:THR209 4.8 23.0 1.0
OH A:TYR306 4.8 28.0 1.0

Calcium binding site 2 out of 2 in 7g6i

Go back to Calcium Binding Sites List in 7g6i
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 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 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:21.7
occ:1.00
 OD1 A:ASP747 2.3 22.8 1.0
OD1 A:ASP743 2.3 24.1 1.0
O A:LEU745 2.3 20.1 1.0
OD1 A:ASP739 2.3 22.2 1.0
OD1 A:ASN741 2.3 25.1 1.0
O A:HOH1431 2.3 25.3 1.0
CG A:ASP743 3.3 25.5 1.0
CG A:ASN741 3.4 26.0 1.0
C A:LEU745 3.5 21.1 1.0
CG A:ASP739 3.5 21.9 1.0
CG A:ASP747 3.5 22.2 1.0
OD2 A:ASP743 3.7 27.0 1.0
ND2 A:ASN741 3.9 26.1 1.0
N A:ASP747 3.9 19.5 1.0
CA A:ASP739 3.9 20.5 1.0
C A:ARG746 4.0 20.9 1.0
N A:LEU745 4.1 21.5 1.0
O A:ARG746 4.1 20.1 1.0
CA A:ASP747 4.2 21.1 1.0
CA A:LEU745 4.2 20.9 1.0
CB A:ASP739 4.3 21.0 1.0
N A:ASP743 4.3 21.9 1.0
OD2 A:ASP747 4.4 23.3 1.0
O A:PHE738 4.4 18.5 1.0
N A:ASN741 4.4 22.5 1.0
C A:ASP739 4.4 21.4 1.0
OD2 A:ASP739 4.4 21.8 1.0
CB A:ASP747 4.5 20.4 1.0
N A:ARG746 4.5 20.7 1.0
CB A:LEU745 4.5 23.7 1.0
CB A:ASP743 4.5 23.2 1.0
O A:HOH1145 4.6 40.0 1.0
OE2 A:GLU751 4.6 36.8 1.0
CA A:ARG746 4.7 20.5 1.0
CB A:ASN741 4.7 24.7 1.0
N A:TYR740 4.7 21.6 1.0
N A:TYR742 4.8 23.0 1.0
CA A:ASP743 4.8 22.2 1.0
N A:GLY744 4.9 22.3 1.0
C A:ASN741 4.9 24.5 1.0
CA A:ASN741 4.9 24.5 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: Sat Feb 8 15:55:17 2025

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