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Calcium in PDB 7g7a: Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm, PDB code: 7g7a 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) 49.01 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.274, 91.77, 120.494, 90, 90, 90
R / Rfree (%) 18.9 / 23.8

Other elements in 7g7a:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 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-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm (pdb code 7g7a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm, PDB code: 7g7a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 7g7a

Go back to Calcium Binding Sites List in 7g7a
Calcium binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 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-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:41.5
occ:1.00
 OG1 A:THR209 1.8 26.2 1.0
OD1 A:ASP171 1.9 28.0 1.0
NE2 A:HIS359 2.0 20.1 1.0
OD2 A:ASP358 2.3 25.1 1.0
CG A:ASP171 2.8 27.5 1.0
CB A:THR209 2.8 21.8 1.0
CE1 A:HIS359 3.0 21.0 1.0
CD2 A:HIS359 3.0 19.5 1.0
CG A:ASP358 3.1 22.3 1.0
OD2 A:ASP171 3.2 33.9 1.0
CG2 A:THR209 3.2 22.3 1.0
CA A:THR209 3.3 22.3 1.0
OD1 A:ASP358 3.4 21.8 1.0
NA A:NA909 3.5 23.0 1.0
O A:HOH1007 3.5 26.3 1.0
N A:THR209 3.9 21.1 1.0
ND1 A:HIS359 4.0 18.4 1.0
OD1 A:ASP311 4.1 23.6 1.0
CG A:HIS359 4.1 19.1 1.0
CB A:ASP171 4.1 23.3 1.0
N A:GLY172 4.2 22.4 1.0
CE1 A:HIS474 4.3 22.8 1.0
CG A:ASP311 4.3 22.8 1.0
CA A:ASP171 4.4 22.5 1.0
CB A:ASP358 4.4 20.6 1.0
ZN A:ZN903 4.4 24.9 1.0
NE2 A:HIS474 4.5 24.3 1.0
O A:HOH1001 4.5 33.6 1.0
C A:THR209 4.6 21.3 1.0
C A:ASP171 4.6 23.3 1.0
C A:LYS208 4.7 22.1 1.0
OD2 A:ASP311 4.7 25.1 1.0
O A:HOH1399 4.8 33.1 1.0
CB A:ASP311 4.8 23.2 1.0

Calcium binding site 2 out of 3 in 7g7a

Go back to Calcium Binding Sites List in 7g7a
Calcium binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 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-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:31.9
occ:1.00
 O A:ASP672 2.3 28.4 1.0
O A:MET675 2.3 26.4 1.0
O A:TYR669 2.3 27.2 1.0
O A:HOH1372 2.4 34.2 1.0
O A:HOH1458 2.5 35.1 1.0
O A:HOH1482 3.0 40.0 1.0
C A:MET675 3.4 26.1 1.0
C A:TYR669 3.5 27.6 1.0
C A:ASP672 3.5 30.7 1.0
N A:MET675 4.1 30.4 1.0
CA A:TYR669 4.2 25.4 1.0
N A:SER676 4.2 23.4 1.0
CA A:LYS673 4.3 34.7 1.0
CA A:SER676 4.3 22.4 1.0
N A:LYS673 4.3 30.1 1.0
CA A:MET675 4.3 25.6 1.0
O A:LYS670 4.4 35.3 1.0
C A:LYS673 4.4 32.7 1.0
N A:LYS670 4.4 29.3 1.0
CA A:ASP672 4.4 30.3 1.0
O A:LYS673 4.6 33.6 1.0
CB A:ASP672 4.6 27.7 1.0
N A:ASP672 4.6 31.9 1.0
CA A:LYS670 4.6 30.9 1.0
C A:LYS670 4.7 31.7 1.0
CB A:TYR669 4.7 23.4 1.0
N A:GLN674 4.8 29.4 1.0
CB A:SER676 4.8 22.0 1.0
C A:GLN674 4.9 32.1 1.0

Calcium binding site 3 out of 3 in 7g7a

Go back to Calcium Binding Sites List in 7g7a
Calcium binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with 2-(4-Chlorophenyl)- 7-Methyl-8-Pentylimidazo[1,2-A]Pyrimidin-5-One, I.E. Smiles O=C1N2C=C(C3CCC(Cl)CC3)N=C2N(C(=C1)C)Ccccc with IC50=0.0671599 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:19.9
occ:1.00
 OD1 A:ASP747 2.2 21.0 1.0
OD1 A:ASP739 2.3 18.1 1.0
O A:HOH1429 2.3 26.6 1.0
O A:LEU745 2.3 18.1 1.0
OD1 A:ASN741 2.3 22.0 1.0
OD1 A:ASP743 2.4 24.0 1.0
CG A:ASP743 3.4 24.7 1.0
CG A:ASN741 3.4 24.0 1.0
CG A:ASP739 3.4 19.0 1.0
C A:LEU745 3.5 19.7 1.0
CG A:ASP747 3.5 21.4 1.0
OD2 A:ASP743 3.8 27.3 1.0
CA A:ASP739 3.9 16.9 1.0
ND2 A:ASN741 3.9 21.4 1.0
N A:ASP747 3.9 20.0 1.0
N A:LEU745 4.1 18.4 1.0
C A:ARG746 4.1 19.2 1.0
CA A:ASP747 4.1 20.8 1.0
CA A:LEU745 4.2 18.7 1.0
CB A:ASP739 4.2 17.3 1.0
N A:ASP743 4.3 19.8 1.0
O A:ARG746 4.3 20.1 1.0
OD2 A:ASP747 4.3 21.6 1.0
OD2 A:ASP739 4.4 19.6 1.0
CB A:ASP747 4.4 20.2 1.0
O A:PHE738 4.4 16.9 1.0
C A:ASP739 4.4 18.5 1.0
CB A:LEU745 4.4 20.0 1.0
N A:ASN741 4.5 20.9 1.0
N A:ARG746 4.5 19.1 1.0
CB A:ASP743 4.6 21.2 1.0
N A:TYR740 4.7 19.1 1.0
CB A:ASN741 4.7 20.5 1.0
CA A:ARG746 4.8 19.0 0.3
OE2 A:GLU751 4.8 44.1 1.0
CA A:ARG746 4.8 18.9 0.7
N A:TYR742 4.8 19.9 1.0
CA A:ASP743 4.8 20.8 1.0
C A:ASN741 4.9 20.7 1.0
N A:GLY744 4.9 20.2 1.0
O A:HOH1436 4.9 41.2 1.0
CA A:ASN741 4.9 20.0 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: Wed Jul 9 22:37:18 2025

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