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Calcium in PDB 7g7i: Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 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-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm, PDB code: 7g7i 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) 46.44 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.903, 92.887, 121.125, 90, 90, 90
R / Rfree (%) 21.4 / 24.2

Other elements in 7g7i:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 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-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm (pdb code 7g7i). 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-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm, PDB code: 7g7i:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7i

Go back to Calcium Binding Sites List in 7g7i
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 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-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:22.2
occ:1.00
 OD1 A:ASP739 2.3 20.2 1.0
O A:LEU745 2.3 19.7 1.0
OD1 A:ASP747 2.3 20.1 1.0
OD1 A:ASP743 2.4 21.9 1.0
OD1 A:ASN741 2.4 22.7 1.0
O A:HOH1334 2.4 25.9 1.0
CG A:ASP743 3.3 22.4 1.0
CG A:ASP739 3.5 20.1 1.0
CG A:ASN741 3.5 26.0 1.0
C A:LEU745 3.5 21.8 1.0
CG A:ASP747 3.6 20.9 1.0
OD2 A:ASP743 3.8 24.2 1.0
ND2 A:ASN741 3.9 29.8 1.0
CA A:ASP739 4.0 18.5 1.0
N A:ASP747 4.0 19.3 1.0
N A:LEU745 4.1 19.1 1.0
C A:ARG746 4.1 20.1 1.0
CB A:ASP739 4.2 19.6 1.0
CA A:ASP747 4.2 20.3 1.0
CA A:LEU745 4.2 19.5 1.0
O A:ARG746 4.3 20.1 1.0
N A:ASP743 4.3 20.9 1.0
OD2 A:ASP739 4.4 19.3 1.0
OD2 A:ASP747 4.4 22.0 1.0
C A:ASP739 4.5 20.8 1.0
CB A:LEU745 4.5 23.6 1.0
O A:PHE738 4.5 19.7 1.0
N A:ASN741 4.5 23.4 1.0
CB A:ASP747 4.5 19.8 1.0
N A:ARG746 4.5 20.7 1.0
CB A:ASP743 4.5 21.8 1.0
OE2 A:GLU751 4.7 32.1 1.0
N A:TYR740 4.7 20.7 1.0
CB A:ASN741 4.8 25.4 1.0
CA A:ARG746 4.8 20.6 1.0
CA A:ASP743 4.8 19.3 1.0
N A:TYR742 4.8 22.4 1.0
C A:ASN741 4.9 23.9 1.0
N A:GLY744 4.9 20.4 1.0
CA A:ASN741 4.9 24.6 1.0

Calcium binding site 2 out of 2 in 7g7i

Go back to Calcium Binding Sites List in 7g7i
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-2-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 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-[6-[1-(2-Methoxyacetyl)Piperidin-4-Yl]-4- Oxoquinazolin-3-Yl]-N-Methylacetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)C1CCN(CC1)C(=O)Coc with IC50=0.0120222 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:43.4
occ:1.00
 OD1 A:ASP171 1.8 30.3 1.0
OG1 A:THR209 2.0 32.1 1.0
NE2 A:HIS359 2.2 20.6 1.0
OD2 A:ASP358 2.2 23.2 1.0
CG A:ASP171 2.8 31.7 1.0
CB A:THR209 2.9 26.0 1.0
CG A:ASP358 3.1 22.1 1.0
CE1 A:HIS359 3.1 19.9 1.0
CG2 A:THR209 3.2 28.6 1.0
CD2 A:HIS359 3.2 19.7 1.0
OD2 A:ASP171 3.2 36.6 1.0
CA A:THR209 3.3 23.6 1.0
OD1 A:ASP358 3.4 21.3 1.0
O A:HOH1069 3.7 39.8 1.0
N A:THR209 3.8 21.6 1.0
CB A:ASP171 4.0 23.1 1.0
ND1 A:HIS359 4.2 19.7 1.0
N A:GLY172 4.2 22.6 1.0
OD1 A:ASP311 4.2 25.7 1.0
CG A:HIS359 4.2 18.8 1.0
CA A:ASP171 4.3 21.9 1.0
CB A:ASP358 4.4 21.3 1.0
CE1 A:HIS474 4.5 22.9 1.0
CG A:ASP311 4.5 25.1 1.0
C A:THR209 4.5 22.7 1.0
C A:ASP171 4.6 22.4 1.0
ZN A:ZN902 4.6 27.4 1.0
C A:LYS208 4.7 22.8 1.0
NE2 A:HIS474 4.7 21.2 1.0
O A:HOH1323 4.8 35.8 1.0
OD2 A:ASP311 4.9 27.0 1.0
O A:THR209 4.9 22.9 1.0
OH A:TYR306 4.9 32.0 1.0
CB A:ASP311 5.0 23.0 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: Sat Feb 8 16:03:01 2025

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