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Calcium in PDB 7g4h: Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm, PDB code: 7g4h 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) 48.83 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.02, 91.785, 120.026, 90, 90, 90
R / Rfree (%) 20 / 23.8

Other elements in 7g4h:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 1 atom
Fluorine (F) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm (pdb code 7g4h). 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm, PDB code: 7g4h:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g4h

Go back to Calcium Binding Sites List in 7g4h
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:26.9
occ:1.00
 OD1 A:ASP747 2.2 23.3 1.0
OD1 A:ASN741 2.3 28.4 1.0
OD1 A:ASP743 2.3 26.5 1.0
O A:LEU745 2.3 23.3 1.0
OD1 A:ASP739 2.4 28.2 1.0
O A:HOH1289 2.4 27.8 1.0
CG A:ASP743 3.2 26.4 1.0
CG A:ASN741 3.4 28.4 1.0
CG A:ASP747 3.5 24.1 1.0
C A:LEU745 3.5 24.5 1.0
CG A:ASP739 3.5 26.2 1.0
OD2 A:ASP743 3.6 27.5 1.0
ND2 A:ASN741 3.9 27.1 1.0
N A:ASP747 3.9 25.0 1.0
CA A:ASP739 3.9 25.3 1.0
C A:ARG746 4.1 26.1 1.0
N A:LEU745 4.1 22.4 1.0
CA A:ASP747 4.1 24.4 1.0
O A:ARG746 4.2 26.0 1.0
CB A:ASP739 4.2 24.6 1.0
CA A:LEU745 4.3 24.0 1.0
N A:ASP743 4.3 25.4 1.0
OD2 A:ASP747 4.3 24.2 1.0
O A:PHE738 4.4 23.2 1.0
CB A:ASP747 4.4 23.4 1.0
N A:ASN741 4.4 25.8 1.0
C A:ASP739 4.5 27.0 1.0
OD2 A:ASP739 4.5 26.7 1.0
CB A:ASP743 4.5 26.1 1.0
N A:ARG746 4.5 23.0 1.0
CB A:LEU745 4.6 24.9 1.0
CB A:ASN741 4.7 26.2 1.0
N A:TYR740 4.7 26.2 1.0
CA A:ARG746 4.8 25.4 1.0
N A:TYR742 4.8 25.1 1.0
CA A:ASP743 4.8 25.6 1.0
C A:ASN741 4.8 26.0 1.0
CA A:ASN741 4.8 26.3 1.0
N A:GLY744 4.9 25.6 1.0
OE2 A:GLU751 4.9 43.9 1.0
O A:HOH1287 4.9 38.4 1.0

Calcium binding site 2 out of 2 in 7g4h

Go back to Calcium Binding Sites List in 7g4h
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:29.0
occ:1.00
 OD1 A:ASP171 1.9 30.4 1.0
OG1 A:THR209 1.9 28.7 1.0
NE2 A:HIS359 2.1 26.9 1.0
OD2 A:ASP358 2.2 29.7 1.0
CG A:ASP171 2.6 31.4 1.0
OD2 A:ASP171 2.7 36.6 1.0
CG A:ASP358 2.9 27.1 1.0
CE1 A:HIS359 3.0 25.4 1.0
CB A:THR209 3.0 28.2 1.0
CD2 A:HIS359 3.0 24.9 1.0
OD1 A:ASP358 3.2 26.0 1.0
CG2 A:THR209 3.4 29.0 1.0
CA A:THR209 3.4 28.5 1.0
CB A:ASP171 3.9 30.3 1.0
N A:THR209 3.9 29.5 1.0
ND1 A:HIS359 4.0 24.6 1.0
CG A:HIS359 4.0 26.6 1.0
N A:GLY172 4.1 25.8 1.0
O A:ACT908 4.2 61.4 1.0
OD1 A:ASP311 4.2 31.4 1.0
CA A:ASP171 4.3 29.0 1.0
CB A:ASP358 4.3 26.5 1.0
CE1 A:HIS474 4.4 25.9 1.0
CG A:ASP311 4.4 29.8 1.0
NE2 A:HIS474 4.4 26.2 1.0
ZN A:ZN902 4.6 30.2 1.0
C A:ASP171 4.6 28.0 1.0
C A:THR209 4.7 27.4 1.0
O A:HOH1003 4.7 30.8 1.0
C A:LYS208 4.8 29.5 1.0
CB A:ASP311 4.8 28.9 1.0
OD2 A:ASP311 4.9 30.8 1.0
OXT A:ACT908 4.9 49.1 1.0
C A:ACT908 5.0 59.5 1.0
O A:THR209 5.0 26.0 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 15:46:25 2025

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