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Fluorine in PDB 7g5w: Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm, PDB code: 7g5w 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) 45.91 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.094, 91.813, 120.216, 90, 90, 90
R / Rfree (%) 19.5 / 23.4

Other elements in 7g5w:

The structure of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Calcium (Ca) 1 atom
Potassium (K) 1 atom
Zinc (Zn) 1 atom
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm (pdb code 7g5w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm, PDB code: 7g5w:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g5w

Go back to Fluorine Binding Sites List in 7g5w
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.5
occ:1.00
 F33 A:XG6901 0.0 44.5 1.0
C32 A:XG6901 1.3 42.8 1.0
F34 A:XG6901 2.1 42.8 1.0
F35 A:XG6901 2.1 42.4 1.0
O31 A:XG6901 2.2 41.6 1.0
C23 A:XG6901 2.7 42.0 1.0
C28 A:XG6901 2.8 41.0 1.0
CB A:ALA217 3.3 23.1 1.0
CA A:ALA217 3.5 22.6 1.0
N A:ALA217 3.7 23.8 1.0
C24 A:XG6901 3.9 41.1 1.0
CD2 A:PHE273 3.9 32.7 1.0
CE2 A:PHE273 4.0 33.6 1.0
CZ3 A:TRP260 4.0 30.5 1.0
C27 A:XG6901 4.0 43.0 1.0
O A:LEU213 4.1 23.3 1.0
C A:LEU216 4.3 23.9 1.0
CB A:LEU216 4.6 23.9 1.0
O A:LEU216 4.6 24.2 1.0
CE3 A:TRP260 4.7 31.4 1.0
C25 A:XG6901 4.9 42.5 1.0
C A:ALA217 4.9 22.7 1.0
C26 A:XG6901 4.9 44.4 1.0
CH2 A:TRP260 4.9 34.0 1.0

Fluorine binding site 2 out of 3 in 7g5w

Go back to Fluorine Binding Sites List in 7g5w
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:42.8
occ:1.00
 F34 A:XG6901 0.0 42.8 1.0
C32 A:XG6901 1.3 42.8 1.0
F33 A:XG6901 2.1 44.5 1.0
F35 A:XG6901 2.2 42.4 1.0
O31 A:XG6901 2.2 41.6 1.0
CB A:LEU216 3.2 23.9 1.0
C23 A:XG6901 3.5 42.0 1.0
C A:LEU216 3.6 23.9 1.0
N A:ALA217 3.7 23.8 1.0
O A:LEU216 3.8 24.2 1.0
CE A:MET512 4.0 25.5 1.0
CA A:ALA217 4.0 22.6 1.0
CA A:LEU216 4.0 23.3 1.0
C28 A:XG6901 4.2 41.0 1.0
CG2 A:ILE167 4.4 23.7 1.0
C24 A:XG6901 4.4 41.1 1.0
CG A:LEU216 4.4 23.9 1.0
O A:LEU213 4.5 23.3 1.0
SD A:MET512 4.5 28.7 1.0
CB A:ALA217 4.5 23.1 1.0
CD1 A:LEU216 4.6 26.0 1.0
CD1 A:ILE167 4.8 29.6 1.0
CD2 A:LEU216 5.0 24.7 1.0

Fluorine binding site 3 out of 3 in 7g5w

Go back to Fluorine Binding Sites List in 7g5w
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Rat Autotaxin in Complex with [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)OCC1CCC(CC1)Oc(F)(F)F with IC50=0.0117482 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:42.4
occ:1.00
 F35 A:XG6901 0.0 42.4 1.0
C32 A:XG6901 1.3 42.8 1.0
F33 A:XG6901 2.1 44.5 1.0
F34 A:XG6901 2.2 42.8 1.0
O31 A:XG6901 2.2 41.6 1.0
C23 A:XG6901 2.8 42.0 1.0
C24 A:XG6901 3.4 41.1 1.0
CG2 A:ILE167 3.5 23.7 1.0
CD1 A:ILE167 3.6 29.6 1.0
CE2 A:PHE273 3.6 33.6 1.0
C28 A:XG6901 3.7 41.0 1.0
CD2 A:PHE273 3.8 32.7 1.0
CB A:ILE167 3.9 24.9 1.0
CG1 A:ILE167 4.2 24.9 1.0
CB A:ALA304 4.4 25.6 1.0
C25 A:XG6901 4.5 42.5 1.0
C27 A:XG6901 4.8 43.0 1.0
CZ A:PHE273 4.8 31.3 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 18:00:08 2025

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