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Calcium in PDB 7g7l: Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm, PDB code: 7g7l was solved by M.Stihle, J.Benz, D.Hunziker, E.Martin-Rainer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.87 / 1.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.116, 91.746, 120.492, 90, 90, 90
R / Rfree (%) 18.9 / 22.4

Other elements in 7g7l:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom
Potassium (K) 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 N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm (pdb code 7g7l). 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 N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm, PDB code: 7g7l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7l

Go back to Calcium Binding Sites List in 7g7l
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 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 N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:45.8
occ:1.00
 OD1 A:ASP171 1.8 28.9 1.0
OG1 A:THR209 1.8 26.0 1.0
NE2 A:HIS359 1.9 20.1 1.0
OD2 A:ASP358 2.3 24.6 1.0
CE1 A:HIS359 2.8 20.4 1.0
CG A:ASP171 2.9 28.2 1.0
CB A:THR209 2.9 22.7 1.0
CD2 A:HIS359 2.9 19.6 1.0
CG A:ASP358 3.0 23.9 1.0
CA A:THR209 3.2 21.3 1.0
CG2 A:THR209 3.3 24.1 1.0
OD1 A:ASP358 3.3 22.3 1.0
OD2 A:ASP171 3.4 34.6 1.0
O A:HOH1057 3.6 34.1 1.0
N A:THR209 3.8 20.2 1.0
ND1 A:HIS359 3.9 19.4 1.0
CG A:HIS359 3.9 19.8 1.0
OD1 A:ASP311 4.1 27.2 1.0
CB A:ASP171 4.1 23.4 1.0
N A:GLY172 4.2 19.5 1.0
CE1 A:HIS474 4.2 25.0 1.0
O A:HOH1002 4.2 34.0 1.0
CA A:ASP171 4.3 21.5 1.0
CB A:ASP358 4.3 21.2 1.0
CG A:ASP311 4.4 25.5 1.0
NE2 A:HIS474 4.4 21.0 1.0
ZN A:ZN906 4.5 24.3 1.0
C A:THR209 4.5 20.8 1.0
C A:LYS208 4.6 22.0 1.0
O A:HOH1394 4.6 25.8 1.0
C A:ASP171 4.6 21.0 1.0
CB A:ASP311 4.9 22.0 1.0
OD2 A:ASP311 4.9 29.2 1.0
O A:THR209 4.9 21.3 1.0
CA A:GLY172 5.0 19.1 1.0
OH A:TYR306 5.0 32.6 1.0

Calcium binding site 2 out of 2 in 7g7l

Go back to Calcium Binding Sites List in 7g7l
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 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 N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[7-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-1-Oxo-3, 4-Dihydroisoquinolin-2-Yl]-N-Methylacetamide, I.E. Smiles Cocc(=O) N1CCC(CC1)C1CC2C(=O)N(Cc(=O)N(C)CC3CCC(C#N)C(Cl)C3)CCC2CC1 with IC50=0.271593 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:20.1
occ:1.00
 OD1 A:ASP739 2.3 20.8 1.0
OD1 A:ASP747 2.3 21.0 1.0
OD1 A:ASP743 2.3 20.8 1.0
O A:LEU745 2.3 19.0 1.0
O A:HOH1429 2.3 24.4 1.0
OD1 A:ASN741 2.4 25.1 1.0
CG A:ASP743 3.3 23.4 1.0
CG A:ASP739 3.4 19.0 1.0
CG A:ASN741 3.4 26.4 1.0
C A:LEU745 3.5 18.9 1.0
CG A:ASP747 3.6 20.1 1.0
OD2 A:ASP743 3.7 23.8 1.0
ND2 A:ASN741 3.9 27.3 1.0
N A:ASP747 4.0 19.8 1.0
CA A:ASP739 4.0 18.2 1.0
N A:LEU745 4.0 18.2 1.0
C A:ARG746 4.1 19.1 1.0
CA A:ASP747 4.1 19.2 1.0
CA A:LEU745 4.2 17.8 1.0
CB A:ASP739 4.2 18.2 1.0
N A:ASP743 4.2 19.9 1.0
O A:ARG746 4.3 21.3 1.0
OD2 A:ASP739 4.4 19.1 1.0
CB A:LEU745 4.4 19.2 1.0
O A:PHE738 4.4 19.2 1.0
OD2 A:ASP747 4.4 22.9 1.0
CB A:ASP747 4.5 20.3 1.0
C A:ASP739 4.5 19.3 1.0
CB A:ASP743 4.5 21.7 1.0
N A:ARG746 4.5 17.7 1.0
N A:ASN741 4.5 20.9 1.0
O A:HOH1343 4.6 37.2 1.0
OE2 A:GLU751 4.6 34.5 1.0
CA A:ARG746 4.7 18.8 1.0
CA A:ASP743 4.8 20.3 1.0
N A:TYR740 4.8 21.0 1.0
N A:TYR742 4.8 22.1 1.0
CB A:ASN741 4.8 23.1 1.0
N A:GLY744 4.9 19.5 1.0
C A:ASN741 4.9 21.9 1.0
CA A:ASN741 5.0 22.3 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 16:03:01 2025

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