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Calcium in PDB 7g6e: Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm, PDB code: 7g6e was solved by M.Stihle, J.Benz, D.Hunziker, R.Goodnow, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.868, 91.785, 119.587, 90, 90, 90
R / Rfree (%) 18.4 / 22.5

Other elements in 7g6e:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
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 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm (pdb code 7g6e). 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 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm, PDB code: 7g6e:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6e

Go back to Calcium Binding Sites List in 7g6e
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 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 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:30.9
occ:1.00
 OG1 A:THR209 1.8 23.5 1.0
OD1 A:ASP171 2.0 27.9 1.0
NE2 A:HIS359 2.1 19.1 1.0
OD2 A:ASP358 2.4 25.2 1.0
O A:HOH1005 2.6 35.5 1.0
CG A:ASP171 2.7 28.6 1.0
CB A:THR209 2.8 22.2 1.0
OD2 A:ASP171 2.9 36.7 1.0
CE1 A:HIS359 3.0 17.5 1.0
CG2 A:THR209 3.1 22.2 1.0
CD2 A:HIS359 3.2 19.1 1.0
CG A:ASP358 3.3 23.1 1.0
CA A:THR209 3.4 21.5 1.0
OD1 A:ASP358 3.5 21.7 1.0
O A:HOH1336 3.6 43.1 1.0
N A:THR209 3.8 20.2 1.0
CB A:ASP171 4.1 23.1 1.0
ND1 A:HIS359 4.1 17.9 1.0
OD1 A:ASP311 4.1 21.4 1.0
CG A:HIS359 4.2 17.9 1.0
CE1 A:HIS474 4.2 18.9 1.0
O A:HOH1002 4.3 28.0 1.0
N A:GLY172 4.3 19.8 1.0
ZN A:ZN906 4.4 22.9 1.0
CG A:ASP311 4.4 22.3 1.0
CA A:ASP171 4.4 21.7 1.0
NE2 A:HIS474 4.5 20.6 1.0
CB A:ASP358 4.5 20.1 1.0
C A:LYS208 4.6 21.4 1.0
O A:HOH1378 4.6 31.5 1.0
C A:THR209 4.7 21.0 1.0
C A:ASP171 4.7 21.3 1.0
OD2 A:ASP311 4.8 24.3 1.0
OH A:TYR306 4.9 28.7 1.0
CB A:ASP311 4.9 20.7 1.0

Calcium binding site 2 out of 2 in 7g6e

Go back to Calcium Binding Sites List in 7g6e
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 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 4-[(7-Benzyl-9- Methyl-8-Oxopurin-2-Yl)Amino]-N-(1-Methylpiperidin-4-Yl)Benzamide, I.E. Smiles N1(C2C(N(C1=O)CC1CCCCC1)Cnc(N2)NC1CCC(C(=O)NC2CCN(CC2)C) CC1)C with IC50=0.0611585 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:19.4
occ:1.00
 O A:LEU745 2.3 19.7 1.0
OD1 A:ASP747 2.3 20.5 1.0
OD1 A:ASP739 2.3 17.6 1.0
O A:HOH1403 2.3 23.5 1.0
OD1 A:ASN741 2.3 21.6 1.0
OD1 A:ASP743 2.4 23.6 1.0
CG A:ASP743 3.3 24.2 1.0
C A:LEU745 3.4 19.8 1.0
CG A:ASN741 3.4 25.1 1.0
CG A:ASP739 3.5 19.4 1.0
CG A:ASP747 3.5 21.1 1.0
OD2 A:ASP743 3.7 25.9 1.0
ND2 A:ASN741 3.9 25.3 1.0
CA A:ASP739 3.9 18.2 1.0
N A:ASP747 4.0 19.3 1.0
C A:ARG746 4.0 19.9 1.0
N A:LEU745 4.1 18.9 1.0
CA A:ASP747 4.1 20.4 1.0
O A:ARG746 4.2 19.1 1.0
CA A:LEU745 4.2 19.1 1.0
CB A:ASP739 4.2 18.7 1.0
N A:ASP743 4.3 19.8 1.0
OD2 A:ASP747 4.4 22.4 1.0
OD2 A:ASP739 4.4 19.0 1.0
CB A:ASP747 4.4 18.9 1.0
C A:ASP739 4.5 19.5 1.0
N A:ASN741 4.5 21.0 1.0
N A:ARG746 4.5 19.7 1.0
CB A:LEU745 4.5 20.1 1.0
O A:PHE738 4.5 18.8 1.0
CB A:ASP743 4.5 22.3 1.0
CA A:ARG746 4.7 19.2 0.3
OE2 A:GLU751 4.7 34.9 1.0
N A:TYR740 4.7 18.9 1.0
CB A:ASN741 4.7 22.3 1.0
O A:HOH1389 4.7 38.1 1.0
CA A:ARG746 4.7 19.4 0.7
N A:TYR742 4.8 20.9 1.0
CA A:ASP743 4.8 20.9 1.0
N A:GLY744 4.8 21.2 1.0
C A:ASN741 4.9 23.2 1.0
CA A:ASN741 4.9 21.7 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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