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Calcium in PDB 7g2s: Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm, PDB code: 7g2s 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) 48.79 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.01, 91.702, 119.881, 90, 90, 90
R / Rfree (%) 21.6 / 26.3

Other elements in 7g2s:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm (pdb code 7g2s). 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm, PDB code: 7g2s:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g2s

Go back to Calcium Binding Sites List in 7g2s
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:21.7
occ:1.00
 OG1 A:THR209 1.8 19.9 1.0
OD1 A:ASP171 1.8 25.1 1.0
OD2 A:ASP358 2.1 20.6 1.0
NE2 A:HIS359 2.1 17.7 1.0
CG A:ASP171 2.8 27.8 1.0
CB A:THR209 2.8 18.0 1.0
CG A:ASP358 3.0 18.4 1.0
CE1 A:HIS359 3.0 17.2 1.0
CD2 A:HIS359 3.0 17.9 1.0
CG2 A:THR209 3.1 20.2 1.0
OD1 A:ASP358 3.2 19.2 1.0
OD2 A:ASP171 3.3 36.8 1.0
CA A:THR209 3.3 17.2 1.0
N A:THR209 3.8 17.1 1.0
CB A:ASP171 4.0 22.5 1.0
ND1 A:HIS359 4.0 17.9 1.0
CG A:HIS359 4.1 16.4 1.0
OD1 A:ASP311 4.2 21.6 1.0
N A:GLY172 4.2 19.4 1.0
O A:HOH1014 4.2 25.8 1.0
CA A:ASP171 4.3 20.9 1.0
CB A:ASP358 4.3 17.2 1.0
CE1 A:HIS474 4.4 18.3 1.0
CG A:ASP311 4.5 18.4 1.0
C A:ASP171 4.6 19.6 1.0
O A:HOH1392 4.6 35.2 1.0
NE2 A:HIS474 4.6 18.1 1.0
C A:THR209 4.6 17.4 1.0
ZN A:ZN905 4.7 19.2 1.0
C A:LYS208 4.7 18.6 1.0
CB A:ASP311 4.8 18.8 1.0

Calcium binding site 2 out of 2 in 7g2s

Go back to Calcium Binding Sites List in 7g2s
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 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-[2-Oxo-2-[4-[[4- (Trifluoromethyl)Phenyl]Methyl]-7,8-Dihydro-5H-Pyrido[4,3- D]Pyrimidin-6-Yl]Ethyl]Sulfanylbenzenesulfonamide, I.E. Smiles C1(C(F)(F)F)Ccc(CC2C3CN(C(=O)CSC4CCC(S(=O)(=O)N)CC4)CCC3NCN2)CC1 with IC50=3.44948 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:16.4
occ:1.00
 OD1 A:ASN741 2.2 19.7 1.0
OD1 A:ASP739 2.2 16.4 1.0
O A:LEU745 2.3 15.3 1.0
OD1 A:ASP743 2.3 20.3 1.0
OD1 A:ASP747 2.3 19.9 1.0
O A:HOH1356 2.4 21.5 1.0
CG A:ASP743 3.3 19.5 1.0
CG A:ASN741 3.3 20.6 1.0
CG A:ASP739 3.4 16.9 1.0
C A:LEU745 3.5 16.4 1.0
CG A:ASP747 3.6 18.8 1.0
OD2 A:ASP743 3.7 21.3 1.0
ND2 A:ASN741 3.9 24.1 1.0
CA A:ASP739 4.0 13.8 1.0
N A:ASP747 4.1 17.5 1.0
N A:LEU745 4.1 16.6 1.0
C A:ARG746 4.1 17.6 1.0
CB A:ASP739 4.1 16.3 1.0
CA A:LEU745 4.2 16.5 1.0
O A:ARG746 4.2 16.1 1.0
CA A:ASP747 4.2 18.1 1.0
N A:ASP743 4.3 18.8 1.0
OD2 A:ASP739 4.4 17.1 1.0
OD2 A:ASP747 4.4 18.1 1.0
CB A:ASP743 4.4 18.9 1.0
N A:ASN741 4.4 17.2 1.0
CB A:LEU745 4.4 19.1 1.0
C A:ASP739 4.5 15.9 1.0
N A:ARG746 4.5 16.2 1.0
CB A:ASP747 4.5 17.1 1.0
O A:PHE738 4.6 14.9 1.0
OE2 A:GLU751 4.6 36.5 1.0
CB A:ASN741 4.6 20.2 1.0
N A:TYR740 4.7 15.5 1.0
CA A:ASP743 4.7 16.7 1.0
CA A:ARG746 4.8 16.6 1.0
N A:TYR742 4.8 18.9 1.0
O A:HOH1330 4.8 36.6 1.0
CA A:ASN741 4.8 18.2 1.0
N A:GLY744 4.8 15.9 1.0
C A:ASN741 4.9 19.0 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 15:35:19 2025

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