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Fluorine 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
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 4 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g5v

Go back to Fluorine Binding Sites List in 7g5v
Fluorine binding site 1 out of 4 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 Fluorine with other atoms in the F 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:F901

b:54.3
occ:1.00
 F31 A:YFT901 0.0 54.3 1.0
C27 A:YFT901 1.3 50.0 1.0
C26 A:YFT901 2.4 50.1 1.0
C28 A:YFT901 2.4 47.6 1.0
O32 A:YFT901 2.7 43.5 1.0
CZ3 A:TRP260 3.4 25.0 1.0
CH2 A:TRP260 3.5 27.4 1.0
C25 A:YFT901 3.6 48.8 1.0
C29 A:YFT901 3.7 46.6 1.0
O A:LEU213 3.8 23.1 1.0
C33 A:YFT901 3.8 45.5 1.0
CB A:ALA217 3.8 20.7 1.0
CE1 A:PHE274 4.0 56.1 1.0
F36 A:YFT901 4.1 45.9 1.0
C30 A:YFT901 4.1 49.3 1.0
CZ A:PHE274 4.2 57.7 1.0
C A:LEU213 4.3 21.9 1.0
CB A:LEU213 4.4 21.2 1.0
F34 A:YFT901 4.5 45.2 1.0
CE3 A:TRP260 4.7 25.9 1.0
F35 A:YFT901 4.7 46.7 1.0
CD2 A:PHE273 4.8 30.3 1.0
CZ2 A:TRP260 4.9 27.2 1.0
N A:TYR214 4.9 23.1 1.0
CA A:LEU213 4.9 21.5 1.0
C24 A:YFT901 4.9 46.8 1.0
CD1 A:PHE274 5.0 54.9 1.0

Fluorine binding site 2 out of 4 in 7g5v

Go back to Fluorine Binding Sites List in 7g5v
Fluorine binding site 2 out of 4 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 Fluorine with other atoms in the F 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:F901

b:45.2
occ:1.00
 F34 A:YFT901 0.0 45.2 1.0
C33 A:YFT901 1.3 45.5 1.0
F36 A:YFT901 2.1 45.9 1.0
F35 A:YFT901 2.2 46.7 1.0
O32 A:YFT901 2.3 43.5 1.0
N A:ALA217 3.2 22.3 1.0
CA A:ALA217 3.3 22.1 1.0
C A:LEU216 3.4 22.1 1.0
CB A:LEU216 3.5 22.8 1.0
C28 A:YFT901 3.5 47.6 1.0
O A:LEU216 3.7 22.1 1.0
CB A:ALA217 3.7 20.7 1.0
CA A:LEU216 4.0 22.6 1.0
CE A:MET512 4.1 22.6 1.0
C29 A:YFT901 4.2 46.6 1.0
O A:LEU213 4.2 23.1 1.0
C27 A:YFT901 4.5 50.0 1.0
F31 A:YFT901 4.5 54.3 1.0
C A:ALA217 4.6 22.9 1.0
CG A:LEU216 4.8 23.6 1.0
SD A:MET512 4.8 25.5 1.0
CE2 A:PHE273 4.9 33.2 1.0
CD1 A:LEU216 4.9 24.3 1.0
CD1 A:ILE167 5.0 25.6 1.0

Fluorine binding site 3 out of 4 in 7g5v

Go back to Fluorine Binding Sites List in 7g5v
Fluorine binding site 3 out of 4 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 Fluorine with other atoms in the F binding site number 3 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:F901

b:46.7
occ:1.00
 F35 A:YFT901 0.0 46.7 1.0
C33 A:YFT901 1.3 45.5 1.0
O32 A:YFT901 2.1 43.5 1.0
F34 A:YFT901 2.2 45.2 1.0
F36 A:YFT901 2.2 45.9 1.0
C29 A:YFT901 2.7 46.6 1.0
C28 A:YFT901 2.7 47.6 1.0
CG2 A:ILE167 3.7 24.2 1.0
CB A:LEU216 4.0 22.8 1.0
C30 A:YFT901 4.0 49.3 1.0
C27 A:YFT901 4.1 50.0 1.0
CD1 A:LEU216 4.2 24.3 1.0
CB A:SER169 4.6 26.1 1.0
CB A:ILE167 4.7 24.5 1.0
CG A:LEU216 4.7 23.6 1.0
F31 A:YFT901 4.7 54.3 1.0
CD1 A:ILE167 4.9 25.6 1.0
O A:LEU213 4.9 23.1 1.0
OG A:SER169 4.9 35.3 1.0
CG1 A:VAL356 4.9 16.9 1.0
N A:ALA217 5.0 22.3 1.0

Fluorine binding site 4 out of 4 in 7g5v

Go back to Fluorine Binding Sites List in 7g5v
Fluorine binding site 4 out of 4 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 Fluorine with other atoms in the F binding site number 4 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:F901

b:45.9
occ:1.00
 F36 A:YFT901 0.0 45.9 1.0
C33 A:YFT901 1.3 45.5 1.0
F34 A:YFT901 2.1 45.2 1.0
F35 A:YFT901 2.2 46.7 1.0
O32 A:YFT901 2.3 43.5 1.0
C28 A:YFT901 2.8 47.6 1.0
C29 A:YFT901 3.2 46.6 1.0
CE2 A:PHE273 3.3 33.2 1.0
CD2 A:PHE273 3.4 30.3 1.0
C27 A:YFT901 3.7 50.0 1.0
CD1 A:ILE167 4.0 25.6 1.0
F31 A:YFT901 4.1 54.3 1.0
C30 A:YFT901 4.3 49.3 1.0
CG2 A:ILE167 4.4 24.2 1.0
CZ A:PHE273 4.6 29.8 1.0
CB A:ALA304 4.6 25.5 1.0
CB A:ALA217 4.6 20.7 1.0
CG A:PHE273 4.7 33.1 1.0
CA A:ALA217 4.7 22.1 1.0
CB A:ILE167 4.7 24.5 1.0
C26 A:YFT901 4.7 50.1 1.0
CZ3 A:TRP260 4.7 25.0 1.0
CG1 A:ILE167 4.8 24.5 1.0
C25 A:YFT901 5.0 48.8 1.0
N A:ALA217 5.0 22.3 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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