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Calcium in PDB 7g7y: Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm, PDB code: 7g7y 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) 43.47 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.785, 92.741, 120.838, 90, 90, 90
R / Rfree (%) 18.1 / 21.6

Other elements in 7g7y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm (pdb code 7g7y). 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-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm, PDB code: 7g7y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7y

Go back to Calcium Binding Sites List in 7g7y
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 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-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:30.6
occ:0.50
 OD1 A:ASP171 1.7 28.2 1.0
OG1 A:THR209 1.8 25.4 1.0
NE2 A:HIS359 2.2 21.2 1.0
OD2 A:ASP358 2.3 23.1 1.0
CG A:ASP171 2.8 27.3 1.0
CB A:THR209 2.8 23.7 1.0
CG2 A:THR209 3.0 25.0 1.0
CE1 A:HIS359 3.0 21.9 1.0
CG A:ASP358 3.1 21.7 1.0
CD2 A:HIS359 3.2 20.9 1.0
OD2 A:ASP171 3.2 35.1 1.0
CA A:THR209 3.3 20.6 1.0
OD1 A:ASP358 3.4 19.8 1.0
O A:HOH1067 3.6 35.0 1.0
N A:THR209 3.9 20.2 1.0
CB A:ASP171 4.0 23.9 1.0
ND1 A:HIS359 4.1 22.4 1.0
CG A:HIS359 4.2 20.7 1.0
OD1 A:ASP311 4.2 24.9 1.0
N A:GLY172 4.3 21.0 1.0
CA A:ASP171 4.3 22.2 1.0
CB A:ASP358 4.4 20.5 1.0
CE1 A:HIS474 4.5 22.6 1.0
O A:HOH1001 4.6 32.1 1.0
CG A:ASP311 4.6 22.8 1.0
C A:THR209 4.6 20.6 1.0
C A:ASP171 4.6 21.1 1.0
ZN A:ZN906 4.7 25.3 1.0
C A:LYS208 4.8 21.8 1.0
NE2 A:HIS474 4.8 22.4 1.0
O A:HOH1458 4.8 32.6 1.0
OH A:TYR306 4.9 28.7 1.0
OD2 A:ASP311 5.0 27.9 1.0
CB A:ASP311 5.0 21.7 1.0
O A:THR209 5.0 20.9 1.0

Calcium binding site 2 out of 2 in 7g7y

Go back to Calcium Binding Sites List in 7g7y
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[[1-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 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-[3-[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methyl]Benzenesulfonamide, I.E. Smiles CC1=Nn(N=N1)CC1CC(C(F)(F)F)CCC1CCC(=O)N1CC[C@@H](CC1) CC1CCC(CC1)S(=O)(=O)N with IC50=0.0117234 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:19.1
occ:1.00
 O A:HOH1416 2.2 23.1 1.0
OD1 A:ASP739 2.3 17.2 1.0
OD1 A:ASP747 2.3 20.3 1.0
O A:LEU745 2.3 19.2 1.0
OD1 A:ASN741 2.3 21.7 1.0
OD1 A:ASP743 2.4 23.3 1.0
CG A:ASP743 3.3 23.3 1.0
CG A:ASN741 3.4 25.0 1.0
CG A:ASP739 3.5 18.4 1.0
C A:LEU745 3.5 19.5 1.0
CG A:ASP747 3.6 20.8 1.0
OD2 A:ASP743 3.7 24.0 1.0
ND2 A:ASN741 3.9 26.0 1.0
N A:ASP747 4.0 17.9 1.0
CA A:ASP739 4.0 16.7 1.0
C A:ARG746 4.1 20.3 1.0
N A:LEU745 4.1 18.3 1.0
CA A:ASP747 4.2 20.0 1.0
O A:ARG746 4.2 19.6 1.0
CB A:ASP739 4.2 18.6 1.0
CA A:LEU745 4.3 18.2 1.0
N A:ASP743 4.3 19.8 1.0
OD2 A:ASP739 4.4 19.2 1.0
OD2 A:ASP747 4.4 20.9 1.0
CB A:ASP747 4.5 19.8 1.0
O A:PHE738 4.5 18.4 1.0
N A:ASN741 4.5 21.4 1.0
CB A:ASP743 4.5 21.1 1.0
CB A:LEU745 4.5 19.3 1.0
C A:ASP739 4.5 19.0 1.0
N A:ARG746 4.5 19.6 1.0
OE2 A:GLU751 4.6 36.0 1.0
N A:TYR740 4.7 19.2 1.0
O A:HOH1406 4.7 37.8 1.0
CB A:ASN741 4.7 23.6 1.0
CA A:ARG746 4.8 19.1 1.0
N A:TYR742 4.8 20.5 1.0
CA A:ASP743 4.8 20.0 1.0
C A:ASN741 4.9 22.6 1.0
N A:GLY744 4.9 18.9 1.0
CA A:ASN741 4.9 22.1 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 16:05:08 2025

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