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Calcium in PDB 7g6l: Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm, PDB code: 7g6l 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) 45.74 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.765, 91.472, 119.345, 90, 90, 90
R / Rfree (%) 18.3 / 21.1

Other elements in 7g6l:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 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 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm (pdb code 7g6l). 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 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm, PDB code: 7g6l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6l

Go back to Calcium Binding Sites List in 7g6l
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 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-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:28.0
occ:1.00
 OD1 A:ASP171 1.8 23.6 1.0
OG1 A:THR209 1.9 22.2 1.0
NE2 A:HIS359 2.1 15.1 1.0
OD2 A:ASP358 2.2 18.8 1.0
O A:HOH1003 2.3 35.9 1.0
CG A:ASP171 2.8 22.9 1.0
CB A:THR209 2.9 20.2 1.0
CE1 A:HIS359 3.0 16.3 1.0
CG A:ASP358 3.0 16.8 1.0
CD2 A:HIS359 3.0 15.6 1.0
OD2 A:ASP171 3.2 33.7 1.0
CG2 A:THR209 3.3 23.5 1.0
OD1 A:ASP358 3.3 15.3 1.0
CA A:THR209 3.3 17.4 1.0
N A:THR209 3.9 16.4 1.0
O A:HOH1011 3.9 36.0 1.0
CB A:ASP171 4.0 17.7 1.0
ND1 A:HIS359 4.1 15.6 1.0
N A:GLY172 4.1 15.6 1.0
OD1 A:ASP311 4.1 20.4 1.0
O A:HOH1044 4.1 33.3 1.0
CG A:HIS359 4.1 15.1 1.0
CA A:ASP171 4.2 17.0 1.0
CB A:ASP358 4.3 14.9 1.0
CE1 A:HIS474 4.4 16.9 1.0
CG A:ASP311 4.4 18.1 1.0
C A:ASP171 4.5 16.3 1.0
ZN A:ZN907 4.5 18.5 1.0
NE2 A:HIS474 4.6 15.8 1.0
C A:THR209 4.6 16.8 1.0
O A:HOH1522 4.7 31.1 1.0
C A:LYS208 4.7 16.3 1.0
CB A:ASP311 4.8 16.6 1.0
OD2 A:ASP311 4.9 20.5 1.0
CA A:GLY172 4.9 15.9 1.0
OH A:TYR306 5.0 24.3 1.0

Calcium binding site 2 out of 2 in 7g6l

Go back to Calcium Binding Sites List in 7g6l
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 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-[6-[4- (Cyclopentanecarbonyl)Piperazin-1-Yl]-4-Oxoquinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, I.E. Smiles C1(Ccc(C(C1)Cl)Cl) Cnc(=O)CN1C(=O)C2CC(CCC2N=C1)N1CCN(CC1)C(=O)C1CCCC1 with IC50=0.00120236 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:15.1
occ:1.00
 OD1 A:ASP747 2.3 16.2 1.0
O A:LEU745 2.3 15.5 1.0
OD1 A:ASP739 2.3 14.3 1.0
OD1 A:ASN741 2.3 17.7 1.0
O A:HOH1469 2.3 21.2 1.0
OD1 A:ASP743 2.4 16.8 1.0
CG A:ASP743 3.3 17.3 1.0
CG A:ASN741 3.4 20.3 1.0
CG A:ASP739 3.4 14.4 1.0
C A:LEU745 3.5 14.3 1.0
CG A:ASP747 3.5 15.1 1.0
OD2 A:ASP743 3.8 19.2 1.0
ND2 A:ASN741 3.8 25.1 1.0
CA A:ASP739 3.9 13.3 1.0
N A:ASP747 4.0 14.3 1.0
C A:ARG746 4.1 15.6 1.0
N A:LEU745 4.1 13.4 1.0
CA A:ASP747 4.1 14.8 1.0
CB A:ASP739 4.2 14.1 1.0
O A:ARG746 4.2 16.5 1.0
CA A:LEU745 4.2 15.0 1.0
N A:ASP743 4.3 15.0 1.0
OD2 A:ASP739 4.4 14.7 1.0
OD2 A:ASP747 4.4 17.4 1.0
CB A:ASP747 4.4 14.9 1.0
O A:PHE738 4.4 13.8 1.0
C A:ASP739 4.4 14.6 1.0
CB A:LEU745 4.4 15.4 1.0
N A:ASN741 4.4 16.1 1.0
N A:ARG746 4.5 14.8 1.0
CB A:ASP743 4.6 16.4 1.0
OE2 A:GLU751 4.6 25.4 1.0
N A:TYR740 4.6 14.1 1.0
CB A:ASN741 4.7 18.1 1.0
N A:TYR742 4.7 15.5 1.0
O A:HOH1466 4.7 30.2 1.0
CA A:ARG746 4.7 15.1 1.0
CA A:ASP743 4.8 15.8 1.0
C A:ASN741 4.8 17.0 1.0
CA A:ASN741 4.9 16.5 1.0
N A:GLY744 4.9 15.3 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 15:55:17 2025

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