Atomistry » Fluorine » PDB 7g2s-7g65 » 7g5w
Atomistry »
  Fluorine »
    PDB 7g2s-7g65 »
      7g5w »

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: Tue Jul 15 20:02:51 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy