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Calcium in PDB 7g5v: Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 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 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm, PDB code: 7g5v 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) 42.99 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.331, 91.977, 120.244, 90, 90, 90
R / Rfree (%) 21 / 25.2

Other elements in 7g5v:

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Potassium (K) 1 atom
Sodium (Na) 1 atom
Fluorine (F) 4 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 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm (pdb code 7g5v). 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 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm, PDB code: 7g5v:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g5v

Go back to Calcium Binding Sites List in 7g5v
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 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 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:80.0
occ:1.00
 OG1 A:THR209 2.0 34.0 1.0
OD1 A:ASP171 2.2 29.7 1.0
NE2 A:HIS359 2.3 22.3 1.0
OD2 A:ASP358 2.8 28.0 1.0
CB A:THR209 3.0 28.7 1.0
CG A:ASP171 3.0 30.7 1.0
CE1 A:HIS359 3.1 22.4 1.0
OD2 A:ASP171 3.2 36.1 1.0
CG2 A:THR209 3.3 25.2 1.0
CA A:THR209 3.3 27.2 1.0
CD2 A:HIS359 3.4 22.2 1.0
CG A:ASP358 3.6 26.5 1.0
C14 A:YFT901 3.6 39.6 1.0
OD1 A:ASP358 3.7 25.8 1.0
N A:THR209 3.8 29.8 1.0
C16 A:YFT901 4.0 39.7 1.0
OD1 A:ASP311 4.0 27.6 1.0
CE1 A:HIS474 4.1 24.1 1.0
ZN A:ZN906 4.1 30.6 1.0
C15 A:YFT901 4.1 42.9 1.0
NE2 A:HIS474 4.2 24.4 1.0
CG A:ASP311 4.2 25.2 1.0
ND1 A:HIS359 4.3 23.1 1.0
N20 A:YFT901 4.3 34.5 1.0
CG A:HIS359 4.4 22.1 1.0
CB A:ASP171 4.4 28.7 1.0
OD2 A:ASP311 4.6 26.8 1.0
C A:LYS208 4.6 27.6 1.0
N A:GLY172 4.7 26.0 1.0
C A:THR209 4.7 28.8 1.0
CB A:ASP311 4.8 24.1 1.0
CA A:ASP171 4.8 25.8 1.0
CB A:ASP358 4.8 25.6 1.0
ND1 A:HIS474 4.9 22.4 1.0
C17 A:YFT901 4.9 42.6 1.0

Calcium binding site 2 out of 2 in 7g5v

Go back to Calcium Binding Sites List in 7g5v
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [3-Fluoro-4- (Trifluoromethoxy)Phenyl]Methyl 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 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 4-[(1H-Benzotriazole-5- Carbonylamino)Methyl]-4-Hydroxypiperidine-1-Carboxylate, I.E. Smiles C1CN(CCC1(O)Cnc(=O)C1CC2C(CC1)Nn=N2)C(=O)OCC1CC(C(CC1)Oc(F)(F)F)F with IC50=0.00632449 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:27.3
occ:1.00
 O A:HOH1182 2.1 31.2 1.0
OD1 A:ASP747 2.2 20.4 1.0
OD1 A:ASN741 2.3 27.5 1.0
O A:LEU745 2.4 30.5 1.0
OD1 A:ASP739 2.4 23.9 1.0
OD1 A:ASP743 2.4 27.7 1.0
CG A:ASP743 3.4 24.9 1.0
CG A:ASN741 3.4 26.2 1.0
CG A:ASP747 3.5 19.7 1.0
CG A:ASP739 3.5 24.5 1.0
C A:LEU745 3.5 26.9 1.0
OD2 A:ASP743 3.8 26.5 1.0
CA A:ASP739 3.9 24.6 1.0
N A:ASP747 3.9 23.3 1.0
ND2 A:ASN741 4.0 25.1 1.0
C A:ARG746 4.0 25.5 1.0
CA A:ASP747 4.1 21.7 1.0
CB A:ASP739 4.2 23.4 1.0
O A:ARG746 4.2 25.6 1.0
N A:LEU745 4.2 24.2 1.0
N A:ASP743 4.2 23.2 1.0
OD2 A:ASP747 4.3 19.9 1.0
C A:ASP739 4.3 26.4 1.0
CA A:LEU745 4.3 25.5 1.0
N A:ASN741 4.3 25.6 1.0
O A:PHE738 4.3 20.9 1.0
CB A:ASP747 4.4 20.0 1.0
OD2 A:ASP739 4.5 23.4 1.0
N A:ARG746 4.5 26.1 1.0
CB A:ASP743 4.5 23.5 1.0
N A:TYR742 4.6 25.9 1.0
CB A:LEU745 4.7 25.2 1.0
CB A:ASN741 4.7 25.4 1.0
N A:TYR740 4.7 27.7 1.0
C A:ASN741 4.7 28.0 1.0
OE2 A:GLU751 4.7 33.9 1.0
CA A:ARG746 4.8 26.1 1.0
CA A:ASN741 4.8 26.3 1.0
CA A:ASP743 4.8 23.8 1.0
O A:ASP739 4.9 26.0 1.0
N A:GLY744 4.9 25.8 1.0
N A:ASP739 5.0 24.5 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 15:51:37 2025

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