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Calcium in PDB 7g7w: Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm, PDB code: 7g7w was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.23 / 1.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.725, 92.758, 120.966, 90, 90, 90
R / Rfree (%) 18.3 / 21.3

Other elements in 7g7w:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm (pdb code 7g7w). 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-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm, PDB code: 7g7w:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7w

Go back to Calcium Binding Sites List in 7g7w
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 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-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:29.0
occ:1.00
 OD1 A:ASP171 1.8 31.7 1.0
OG1 A:THR209 1.9 18.4 1.0
NE2 A:HIS359 2.1 15.9 1.0
OD2 A:ASP358 2.3 17.6 1.0
CB A:THR209 2.8 18.0 1.0
CG A:ASP171 2.9 24.6 1.0
CE1 A:HIS359 3.0 16.0 1.0
CD2 A:HIS359 3.0 15.6 1.0
CG A:ASP358 3.1 17.2 1.0
CG2 A:THR209 3.1 19.7 1.0
CA A:THR209 3.3 16.2 1.0
OD1 A:ASP358 3.4 15.4 1.0
OD2 A:ASP171 3.4 34.1 1.0
O A:HOH1374 3.8 37.8 1.0
N A:THR209 3.9 15.7 1.0
ND1 A:HIS359 4.1 16.5 1.0
CG A:HIS359 4.1 14.2 1.0
CB A:ASP171 4.1 18.4 1.0
OD1 A:ASP311 4.1 19.1 1.0
N A:GLY172 4.2 15.3 1.0
CB A:ASP358 4.3 15.4 1.0
CA A:ASP171 4.3 16.7 1.0
CE1 A:HIS474 4.5 17.4 1.0
O A:HOH1010 4.6 24.4 1.0
C A:THR209 4.6 16.8 1.0
CG A:ASP311 4.6 17.9 1.0
ZN A:ZN906 4.7 19.0 1.0
C A:ASP171 4.7 15.3 1.0
O A:HOH1532 4.7 34.6 1.0
C A:LYS208 4.7 15.7 1.0
NE2 A:HIS474 4.7 15.8 1.0
OH A:TYR306 4.9 24.7 1.0

Calcium binding site 2 out of 2 in 7g7w

Go back to Calcium Binding Sites List in 7g7w
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 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-[4-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazine-1-Carbonyl]Benzenesulfonamide, I.E. Smiles C(=O)(N1CCN(CC1)C(=O)C1CCC(CC1)S(=O)(=O)N) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0212583 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:14.1
occ:1.00
 OD1 A:ASP747 2.3 15.7 1.0
O A:LEU745 2.3 13.8 1.0
OD1 A:ASN741 2.3 17.8 1.0
O A:HOH1460 2.3 18.9 1.0
OD1 A:ASP739 2.3 15.0 1.0
OD1 A:ASP743 2.4 15.2 1.0
CG A:ASP743 3.3 16.7 1.0
CG A:ASN741 3.4 17.9 1.0
CG A:ASP739 3.5 13.9 1.0
C A:LEU745 3.5 14.4 1.0
CG A:ASP747 3.5 15.0 1.0
OD2 A:ASP743 3.8 17.0 1.0
ND2 A:ASN741 3.8 21.4 1.0
CA A:ASP739 4.0 12.9 1.0
N A:ASP747 4.0 14.8 1.0
C A:ARG746 4.1 15.5 1.0
N A:LEU745 4.1 14.3 1.0
CA A:ASP747 4.2 15.2 1.0
CB A:ASP739 4.2 14.2 1.0
O A:ARG746 4.3 15.9 1.0
CA A:LEU745 4.3 14.8 1.0
N A:ASP743 4.3 14.8 1.0
CB A:ASP747 4.4 15.7 1.0
OD2 A:ASP747 4.4 14.7 1.0
OD2 A:ASP739 4.4 14.0 1.0
O A:PHE738 4.5 13.6 1.0
C A:ASP739 4.5 13.7 1.0
CB A:ASP743 4.5 15.2 1.0
N A:ARG746 4.5 14.9 1.0
N A:ASN741 4.6 15.6 1.0
CB A:LEU745 4.6 16.2 1.0
OE2 A:GLU751 4.6 26.7 1.0
O A:HOH1341 4.7 26.4 1.0
CB A:ASN741 4.7 16.6 1.0
N A:TYR740 4.7 14.0 1.0
CA A:ARG746 4.8 16.1 1.0
CA A:ASP743 4.8 14.8 1.0
N A:TYR742 4.8 15.8 1.0
C A:ASN741 4.9 16.6 1.0
CA A:ASN741 4.9 16.2 1.0
N A:GLY744 5.0 14.3 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 16:05:19 2025

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