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Calcium in PDB 7g2g: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm, PDB code: 7g2g 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) 48.48 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.661, 91.242, 118.982, 90, 90, 90
R / Rfree (%) 18.4 / 23.4

Other elements in 7g2g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm also contains other interesting chemical elements:

Fluorine (F) 4 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 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm (pdb code 7g2g). 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 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm, PDB code: 7g2g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2g

Go back to Calcium Binding Sites List in 7g2g
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 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 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:67.4
occ:1.00
 OD1 A:ASP171 1.8 42.5 1.0
OG1 A:THR209 2.0 30.5 1.0
NE2 A:HIS359 2.2 32.9 1.0
OD2 A:ASP358 2.4 37.9 1.0
CG A:ASP171 2.8 35.6 1.0
CE1 A:HIS359 2.9 30.6 1.0
CB A:THR209 3.0 29.9 1.0
CG A:ASP358 3.1 35.3 1.0
CD2 A:HIS359 3.2 30.9 1.0
CG2 A:THR209 3.2 31.5 1.0
OD2 A:ASP171 3.2 44.4 1.0
O A:HOH1048 3.3 44.3 1.0
OD1 A:ASP358 3.3 27.9 1.0
CA A:THR209 3.4 31.2 1.0
N A:THR209 3.9 31.1 1.0
ND1 A:HIS359 4.0 34.3 1.0
CB A:ASP171 4.0 36.4 1.0
OD1 A:ASP311 4.1 25.2 1.0
N A:GLY172 4.2 30.8 1.0
CG A:HIS359 4.2 30.0 1.0
CG A:ASP311 4.3 31.8 1.0
CA A:ASP171 4.3 33.1 1.0
CE1 A:HIS474 4.4 34.4 1.0
CB A:ASP358 4.5 30.9 1.0
ZN A:ZN906 4.5 33.6 1.0
NE2 A:HIS474 4.5 31.5 1.0
O A:HOH1001 4.6 37.5 1.0
C A:ASP171 4.6 32.9 1.0
CB A:ASP311 4.7 33.3 1.0
OD2 A:ASP311 4.7 30.6 1.0
C A:THR209 4.7 32.0 1.0
C A:LYS208 4.7 33.2 1.0
O A:HOH1247 4.7 40.7 1.0
OH A:TYR306 4.8 38.5 1.0
CA A:GLY172 5.0 31.8 1.0

Calcium binding site 2 out of 2 in 7g2g

Go back to Calcium Binding Sites List in 7g2g
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 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 3-Fluoro-4-[[4-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperazin-1-Yl]Methyl]Benzenesulfonamide, I.E. Smiles N1(Ccn(CC1)CC1C(Cc(S(=O)(=O)N)CC1)F)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0203648 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:29.7
occ:1.00
 O A:HOH1211 2.2 37.7 1.0
OD1 A:ASP747 2.2 30.7 1.0
OD1 A:ASP743 2.3 33.2 1.0
OD1 A:ASN741 2.3 28.8 1.0
O A:LEU745 2.3 28.3 1.0
OD1 A:ASP739 2.3 28.0 1.0
CG A:ASP743 3.2 31.2 1.0
CG A:ASN741 3.3 31.9 1.0
CG A:ASP747 3.4 30.6 1.0
CG A:ASP739 3.5 28.2 1.0
C A:LEU745 3.5 31.4 1.0
OD2 A:ASP743 3.7 32.4 1.0
ND2 A:ASN741 3.7 35.2 1.0
N A:ASP747 3.9 28.3 1.0
CA A:ASP739 3.9 30.1 1.0
C A:ARG746 4.1 31.5 1.0
N A:LEU745 4.1 28.5 1.0
CA A:ASP747 4.2 27.8 1.0
CB A:ASP739 4.2 28.2 1.0
OD2 A:ASP747 4.2 32.6 1.0
CA A:LEU745 4.2 29.8 1.0
N A:ASP743 4.2 26.8 1.0
O A:ARG746 4.3 29.9 1.0
OD2 A:ASP739 4.4 30.0 1.0
CB A:ASP747 4.4 26.9 1.0
N A:ASN741 4.4 28.7 1.0
O A:PHE738 4.4 27.5 1.0
CB A:ASP743 4.4 28.8 1.0
C A:ASP739 4.5 29.4 1.0
CB A:LEU745 4.5 30.6 1.0
N A:ARG746 4.5 31.5 1.0
CB A:ASN741 4.6 28.4 1.0
N A:TYR742 4.7 28.8 1.0
CA A:ASP743 4.8 28.7 1.0
N A:TYR740 4.8 29.8 1.0
CA A:ARG746 4.8 30.7 1.0
N A:GLY744 4.8 30.9 1.0
C A:ASN741 4.8 31.8 1.0
OE2 A:GLU751 4.8 56.4 1.0
CA A:ASN741 4.9 30.4 1.0
O A:ASP739 5.0 28.1 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 15:33:32 2025

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