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Calcium in PDB 7g6r: Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm, PDB code: 7g6r 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) 45.87 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.722, 91.73, 119.255, 90, 90, 90
R / Rfree (%) 19.6 / 22.6

Other elements in 7g6r:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm (pdb code 7g6r). 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-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm, PDB code: 7g6r:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g6r

Go back to Calcium Binding Sites List in 7g6r
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 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-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:21.5
occ:1.00
 OG1 A:THR209 1.8 16.8 1.0
OD1 A:ASP171 1.9 20.0 1.0
NE2 A:HIS359 2.1 11.6 1.0
OD2 A:ASP358 2.2 17.8 1.0
CG A:ASP171 2.7 22.2 1.0
CB A:THR209 2.9 14.9 1.0
CE1 A:HIS359 3.0 13.2 1.0
CD2 A:HIS359 3.1 12.0 1.0
CG A:ASP358 3.1 15.8 1.0
OD2 A:ASP171 3.1 33.5 1.0
CG2 A:THR209 3.3 17.9 1.0
OD1 A:ASP358 3.3 13.4 1.0
CA A:THR209 3.4 13.2 1.0
N A:THR209 3.8 12.7 1.0
CB A:ASP171 4.0 17.3 1.0
OD2 A:ASP311 4.0 18.9 1.0
ND1 A:HIS359 4.0 12.8 1.0
CG A:HIS359 4.1 11.6 1.0
O A:HOH1047 4.2 24.1 1.0
N A:GLY172 4.2 14.6 1.0
CA A:ASP171 4.3 15.3 1.0
CE1 A:HIS474 4.4 13.6 1.0
CG A:ASP311 4.4 16.9 1.0
CB A:ASP358 4.4 14.6 1.0
ZN A:ZN905 4.5 16.9 1.0
O A:HOH1472 4.5 29.7 1.0
C A:ASP171 4.6 14.6 1.0
NE2 A:HIS474 4.6 12.2 1.0
C A:LYS208 4.7 12.8 1.0
C A:THR209 4.7 14.1 1.0
CB A:ASP311 4.8 14.7 1.0
OH A:TYR306 4.9 28.9 1.0
OD1 A:ASP311 4.9 20.0 1.0

Calcium binding site 2 out of 2 in 7g6r

Go back to Calcium Binding Sites List in 7g6r
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 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-(1- Benzylpyrrolo[2,3-B]Pyridin-3-Yl)-N-Methyl-3-Nitrobenzamide, I.E. Smiles C1(=Cn(C2C1CCCN2)CC1CCCCC1)C1CCC(CC1N(=O)=O)C(=O)Nc with IC50=0.0467384 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:13.3
occ:1.00
 O A:LEU745 2.3 14.1 1.0
OD1 A:ASP747 2.3 15.1 1.0
O A:HOH1449 2.3 20.4 1.0
OD1 A:ASN741 2.3 15.3 1.0
OD1 A:ASP739 2.3 13.3 1.0
OD1 A:ASP743 2.4 16.5 1.0
CG A:ASP743 3.4 19.0 1.0
CG A:ASN741 3.4 17.5 1.0
C A:LEU745 3.4 13.2 1.0
CG A:ASP739 3.5 13.8 1.0
CG A:ASP747 3.5 14.7 1.0
OD2 A:ASP743 3.8 19.5 1.0
ND2 A:ASN741 3.8 19.3 1.0
CA A:ASP739 3.9 12.0 1.0
N A:ASP747 4.0 12.7 1.0
C A:ARG746 4.0 14.1 1.0
N A:LEU745 4.1 13.1 1.0
CA A:ASP747 4.1 13.1 1.0
O A:ARG746 4.2 13.1 1.0
CB A:ASP739 4.2 12.6 1.0
CA A:LEU745 4.2 13.5 1.0
N A:ASP743 4.3 15.6 1.0
OD2 A:ASP747 4.4 16.2 1.0
C A:ASP739 4.4 13.7 1.0
OD2 A:ASP739 4.4 13.7 1.0
CB A:ASP747 4.4 14.0 1.0
O A:PHE738 4.4 12.3 1.0
N A:ASN741 4.5 14.9 1.0
N A:ARG746 4.5 12.9 1.0
CB A:LEU745 4.5 14.3 1.0
CB A:ASP743 4.6 16.4 1.0
OE2 A:GLU751 4.7 31.7 1.0
N A:TYR740 4.7 14.2 1.0
CB A:ASN741 4.7 14.4 1.0
CA A:ARG746 4.7 13.5 1.0
O A:HOH1430 4.7 32.0 1.0
N A:TYR742 4.8 14.9 1.0
CA A:ASP743 4.8 16.2 1.0
C A:ASN741 4.9 15.4 1.0
CA A:ASN741 4.9 14.3 1.0
N A:GLY744 4.9 14.2 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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