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Calcium in PDB 7g6v: Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm, PDB code: 7g6v 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) 46.15 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.712, 92.306, 119.9, 90, 90, 90
R / Rfree (%) 19.8 / 25.1

Other elements in 7g6v:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 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-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm (pdb code 7g6v). 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-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm, PDB code: 7g6v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6v

Go back to Calcium Binding Sites List in 7g6v
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 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-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:36.9
occ:1.00
 OG1 A:THR209 1.8 40.6 1.0
OD1 A:ASP171 1.9 36.8 1.0
NE2 A:HIS359 2.2 34.7 1.0
OD2 A:ASP358 2.4 41.9 1.0
CG A:ASP171 2.6 36.7 1.0
OD2 A:ASP171 2.7 39.6 1.0
CB A:THR209 3.0 39.1 1.0
O A:HOH1003 3.0 47.1 1.0
CE1 A:HIS359 3.0 34.0 1.0
CD2 A:HIS359 3.2 34.0 1.0
CG A:ASP358 3.3 39.3 1.0
CG2 A:THR209 3.5 41.7 1.0
CA A:THR209 3.5 37.3 1.0
OD1 A:ASP358 3.6 39.3 1.0
O A:HOH1004 3.9 54.4 1.0
N A:THR209 3.9 38.5 1.0
CB A:ASP171 4.0 36.7 1.0
ND1 A:HIS359 4.2 35.0 1.0
ZN A:ZN906 4.2 47.0 1.0
OD1 A:ASP311 4.2 42.0 1.0
NE2 A:HIS474 4.3 38.5 1.0
CE1 A:HIS474 4.3 36.0 1.0
CG A:HIS359 4.3 33.7 1.0
CG A:ASP311 4.3 41.1 1.0
N A:GLY172 4.5 36.5 1.0
OD2 A:ASP311 4.5 41.6 1.0
CA A:ASP171 4.5 37.1 1.0
CB A:ASP358 4.7 36.5 1.0
C A:LYS208 4.7 37.6 1.0
CB A:ASP311 4.8 39.3 1.0
C A:THR209 4.9 37.7 1.0
C A:ASP171 4.9 37.3 1.0
OH A:TYR306 4.9 42.9 1.0
O A:HOH1237 5.0 55.5 1.0

Calcium binding site 2 out of 2 in 7g6v

Go back to Calcium Binding Sites List in 7g6v
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with N-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 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-Methyl-4-(5- Methyl-6-Propoxypyridin-3-Yl)-3-Nitrobenzamide, I.E. Smiles C1(C2CCC(CC2N(=O)=O)C(=O)Nc)Cc(C(NC1)Occc)C with IC50=2.80537 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:38.4
occ:1.00
 O A:HOH1155 2.0 43.4 1.0
OD1 A:ASP747 2.2 33.2 1.0
O A:LEU745 2.3 35.5 1.0
OD1 A:ASN741 2.3 40.9 1.0
OD1 A:ASP743 2.3 40.8 1.0
OD1 A:ASP739 2.4 37.6 1.0
CG A:ASP743 3.3 39.0 1.0
C A:LEU745 3.4 37.8 1.0
CG A:ASN741 3.4 37.8 1.0
CG A:ASP747 3.4 37.2 1.0
CG A:ASP739 3.5 37.1 1.0
OD2 A:ASP743 3.6 40.2 1.0
ND2 A:ASN741 3.8 36.1 1.0
N A:ASP747 3.9 37.7 1.0
N A:LEU745 3.9 37.0 1.0
CA A:ASP739 4.0 35.7 1.0
CA A:LEU745 4.0 37.9 1.0
C A:ARG746 4.1 38.5 1.0
CA A:ASP747 4.2 36.9 1.0
CB A:ASP739 4.2 34.4 1.0
N A:ASP743 4.2 35.4 1.0
OD2 A:ASP747 4.3 37.1 1.0
CB A:LEU745 4.3 36.1 1.0
O A:ARG746 4.3 38.1 1.0
O A:PHE738 4.4 35.8 1.0
OD2 A:ASP739 4.4 35.8 1.0
CB A:ASP747 4.4 37.5 1.0
N A:ARG746 4.4 38.3 1.0
C A:ASP739 4.5 36.5 1.0
N A:ASN741 4.5 36.9 1.0
CB A:ASP743 4.6 35.9 1.0
CB A:ASN741 4.7 35.2 1.0
N A:TYR742 4.7 38.2 1.0
CA A:ARG746 4.7 39.9 1.0
N A:GLY744 4.7 35.0 1.0
CA A:ASP743 4.8 36.4 1.0
C A:ASN741 4.8 39.1 1.0
CA A:ASN741 4.9 36.9 1.0
N A:TYR740 4.9 37.4 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 15:59:10 2025

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