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Calcium in PDB 7g7k: Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 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]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm, PDB code: 7g7k 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) 46.02 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.08, 92.048, 120.021, 90, 90, 90
R / Rfree (%) 19.2 / 23

Other elements in 7g7k:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 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]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm (pdb code 7g7k). 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]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm, PDB code: 7g7k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7k

Go back to Calcium Binding Sites List in 7g7k
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 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]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:42.2
occ:1.00
 OD1 A:ASP171 1.8 28.5 1.0
OG1 A:THR209 1.9 29.1 1.0
NE2 A:HIS359 2.1 22.0 1.0
OD2 A:ASP358 2.3 25.2 1.0
CG A:ASP171 2.7 30.6 1.0
CE1 A:HIS359 2.9 22.4 1.0
CB A:THR209 3.0 26.1 1.0
OD2 A:ASP171 3.0 43.1 1.0
CD2 A:HIS359 3.1 22.1 1.0
CG A:ASP358 3.1 25.7 1.0
CG2 A:THR209 3.2 27.6 1.0
CA A:THR209 3.3 23.8 1.0
OD1 A:ASP358 3.4 23.1 1.0
O A:HOH1143 3.5 32.4 1.0
N A:THR209 3.9 24.2 1.0
CB A:ASP171 4.0 25.2 1.0
ND1 A:HIS359 4.0 21.0 1.0
OD1 A:ASP311 4.1 25.6 1.0
CG A:HIS359 4.1 21.3 1.0
N A:GLY172 4.2 21.6 1.0
CA A:ASP171 4.3 22.2 1.0
CE1 A:HIS474 4.3 22.5 1.0
CG A:ASP311 4.4 23.4 1.0
O A:HOH1002 4.4 33.1 1.0
CB A:ASP358 4.5 24.2 1.0
ZN A:ZN906 4.5 25.6 1.0
NE2 A:HIS474 4.5 20.5 1.0
C A:ASP171 4.6 21.3 1.0
O A:HOH1410 4.6 30.4 1.0
C A:THR209 4.6 23.5 1.0
C A:LYS208 4.7 23.4 1.0
CB A:ASP311 4.8 22.5 1.0
OD2 A:ASP311 4.9 27.6 1.0
OH A:TYR306 4.9 31.3 1.0

Calcium binding site 2 out of 2 in 7g7k

Go back to Calcium Binding Sites List in 7g7k
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-[(3-Chloro-4- Cyanophenyl)Methyl]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 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]-N-Methyl-2-[6-[1-(Oxetane-2-Carbonyl)Piperidin-4- Yl]-4-Oxoquinazolin-3-Yl]Acetamide, I.E. Smiles C1(CCC2C(C1)C(=O) N(C=N2)Cc(=O)N(CC1CC(C(CC1)C#N)Cl)C)[C@H]1CCN(CC1)C(=O)[C@H]1OCC1 with IC50=0.0239157 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:21.9
occ:1.00
 OD1 A:ASP743 2.3 23.3 1.0
OD1 A:ASP747 2.3 20.4 1.0
O A:LEU745 2.3 21.3 1.0
OD1 A:ASP739 2.3 22.4 1.0
O A:HOH1330 2.4 25.6 1.0
OD1 A:ASN741 2.4 26.5 1.0
CG A:ASP743 3.3 24.0 1.0
C A:LEU745 3.4 20.9 1.0
CG A:ASP739 3.5 21.1 1.0
CG A:ASN741 3.5 28.5 1.0
CG A:ASP747 3.6 21.3 1.0
OD2 A:ASP743 3.8 25.9 1.0
CA A:ASP739 3.9 17.6 1.0
N A:ASP747 3.9 21.1 1.0
ND2 A:ASN741 3.9 27.2 1.0
C A:ARG746 4.0 20.5 1.0
N A:LEU745 4.0 20.6 1.0
CA A:ASP747 4.2 22.6 1.0
CA A:LEU745 4.2 18.7 1.0
CB A:ASP739 4.2 18.8 1.0
O A:ARG746 4.2 20.3 1.0
N A:ASP743 4.3 21.9 1.0
OD2 A:ASP739 4.4 20.3 1.0
OD2 A:ASP747 4.4 24.2 1.0
CB A:LEU745 4.4 23.4 1.0
O A:PHE738 4.4 18.0 1.0
C A:ASP739 4.4 21.5 1.0
CB A:ASP747 4.5 20.6 1.0
N A:ARG746 4.5 19.4 1.0
CB A:ASP743 4.5 23.9 1.0
N A:ASN741 4.5 24.7 1.0
OE2 A:GLU751 4.6 36.9 1.0
O A:HOH1448 4.7 37.5 1.0
CA A:ARG746 4.7 20.6 1.0
N A:TYR742 4.8 23.6 1.0
N A:TYR740 4.8 23.0 1.0
CA A:ASP743 4.8 23.4 1.0
CB A:ASN741 4.8 25.4 1.0
N A:GLY744 4.9 22.4 1.0
C A:ASN741 4.9 24.1 1.0
CA A:ASN741 5.0 25.1 1.0
O A:ASP739 5.0 20.4 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 16:03:12 2025

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