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Calcium in PDB 7g5t: Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm, PDB code: 7g5t was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.72 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.799, 91.434, 119.561, 90, 90, 90
R / Rfree (%) 19.7 / 23.2

Other elements in 7g5t:

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm (pdb code 7g5t). 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- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm, PDB code: 7g5t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g5t

Go back to Calcium Binding Sites List in 7g5t
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 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- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:36.8
occ:1.00
 OD1 A:ASP171 1.8 25.4 1.0
OG1 A:THR209 2.1 25.1 1.0
OD2 A:ASP358 2.2 22.1 1.0
NE2 A:HIS359 2.2 18.5 1.0
CG A:ASP171 2.8 27.8 1.0
CB A:THR209 2.9 23.3 1.0
CG A:ASP358 3.0 20.2 1.0
CE1 A:HIS359 3.0 17.7 1.0
CG2 A:THR209 3.1 24.0 1.0
CD2 A:HIS359 3.2 18.0 1.0
OD2 A:ASP171 3.2 35.4 1.0
OD1 A:ASP358 3.2 19.6 1.0
CA A:THR209 3.3 22.3 1.0
N A:THR209 3.9 21.7 1.0
CB A:ASP171 4.0 24.4 1.0
ND1 A:HIS359 4.1 18.6 1.0
C15 A:Y6I901 4.1 61.5 1.0
CG A:HIS359 4.2 18.4 1.0
N A:GLY172 4.2 22.3 1.0
CA A:ASP171 4.3 23.3 1.0
OD1 A:ASP311 4.3 23.7 1.0
CB A:ASP358 4.3 19.1 1.0
CE1 A:HIS474 4.4 19.1 1.0
CG A:ASP311 4.6 23.8 1.0
C A:THR209 4.6 21.9 1.0
O A:HOH1003 4.6 33.8 1.0
C A:ASP171 4.6 23.1 1.0
ZN A:ZN905 4.7 24.5 1.0
NE2 A:HIS474 4.7 19.0 1.0
C18 A:Y6I901 4.7 62.5 1.0
N19 A:Y6I901 4.7 56.3 1.0
C A:LYS208 4.7 23.0 1.0
OH A:TYR306 4.7 29.4 1.0
C14 A:Y6I901 4.8 61.9 1.0
CB A:ASP311 4.9 23.4 1.0
O A:THR209 5.0 21.1 1.0

Calcium binding site 2 out of 2 in 7g5t

Go back to Calcium Binding Sites List in 7g5t
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 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- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-4,5,7,8-Tetrahydropyrazolo[1,5-D][1, 4]Diazepine-6-Carboxylate, I.E. Smiles C1CN2C(=Cc(=N2)C(=O) N2CCC3=C(C2)N=NN3)CCN1C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.0113804 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:20.6
occ:1.00
 OD1 A:ASN741 2.3 21.3 1.0
OD1 A:ASP747 2.3 19.6 1.0
OD1 A:ASP743 2.4 19.6 1.0
O A:LEU745 2.4 19.3 1.0
OD1 A:ASP739 2.4 18.9 1.0
O A:HOH1342 2.4 22.6 1.0
CG A:ASP743 3.3 19.3 1.0
CG A:ASN741 3.4 21.1 1.0
C A:LEU745 3.5 19.6 1.0
CG A:ASP739 3.5 18.6 1.0
CG A:ASP747 3.6 18.4 1.0
OD2 A:ASP743 3.7 20.6 1.0
ND2 A:ASN741 3.9 20.6 1.0
N A:ASP747 3.9 18.6 1.0
CA A:ASP739 4.0 17.5 1.0
C A:ARG746 4.1 20.2 1.0
CA A:ASP747 4.1 19.4 1.0
N A:LEU745 4.1 17.4 1.0
O A:ARG746 4.2 19.7 1.0
N A:ASP743 4.2 20.0 1.0
CB A:ASP739 4.3 18.3 1.0
CA A:LEU745 4.3 18.7 1.0
O A:PHE738 4.4 16.8 1.0
OD2 A:ASP739 4.4 18.8 1.0
OD2 A:ASP747 4.4 19.9 1.0
CB A:ASP747 4.4 18.1 1.0
C A:ASP739 4.5 19.0 1.0
N A:ASN741 4.5 18.8 1.0
CB A:ASP743 4.5 19.1 1.0
N A:ARG746 4.5 19.1 1.0
CB A:LEU745 4.6 20.1 1.0
OE2 A:GLU751 4.6 32.4 1.0
N A:TYR740 4.7 18.8 1.0
CB A:ASN741 4.7 19.7 1.0
N A:TYR742 4.7 19.0 1.0
CA A:ARG746 4.8 19.7 1.0
O A:HOH1306 4.8 37.0 1.0
CA A:ASP743 4.8 18.8 1.0
N A:GLY744 4.8 19.1 1.0
C A:ASN741 4.9 19.6 1.0
CA A:ASN741 4.9 19.4 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: Wed Jul 9 22:30:36 2025

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