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Fluorine in PDB 7g6d: Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm, PDB code: 7g6d 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) 45.84 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.142, 91.682, 119.036, 90, 90, 90
R / Rfree (%) 19.2 / 23

Other elements in 7g6d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm also contains other interesting chemical elements:

Sodium (Na) 1 atom
Calcium (Ca) 2 atoms
Potassium (K) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm (pdb code 7g6d). 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm, PDB code: 7g6d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g6d

Go back to Fluorine Binding Sites List in 7g6d
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:54.9
occ:1.00
 F27 A:Y4Z901 0.0 54.9 1.0
C26 A:Y4Z901 1.3 50.2 1.0
F29 A:Y4Z901 2.1 43.1 1.0
F28 A:Y4Z901 2.2 41.5 1.0
O25 A:Y4Z901 2.3 44.1 1.0
C20 A:Y4Z901 3.0 40.5 1.0
C21 A:Y4Z901 3.3 37.4 1.0
CD2 A:PHE273 3.3 30.1 1.0
CE2 A:PHE273 3.4 33.0 1.0
CB A:ALA217 3.5 18.0 1.0
CZ3 A:TRP260 3.8 26.3 1.0
CA A:ALA217 3.8 18.6 1.0
C19 A:Y4Z901 4.0 39.0 1.0
CE3 A:TRP260 4.2 27.4 1.0
N A:ALA217 4.3 17.5 1.0
C16 A:Y4Z901 4.4 33.1 1.0
O A:LEU213 4.6 18.4 1.0
CG A:PHE273 4.6 30.1 1.0
CZ A:PHE273 4.8 30.8 1.0
C A:LEU216 4.9 18.6 1.0
CH2 A:TRP260 4.9 27.0 1.0
CD1 A:ILE167 5.0 23.8 1.0

Fluorine binding site 2 out of 3 in 7g6d

Go back to Fluorine Binding Sites List in 7g6d
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:41.5
occ:1.00
 F28 A:Y4Z901 0.0 41.5 1.0
C26 A:Y4Z901 1.4 50.2 1.0
F29 A:Y4Z901 2.1 43.1 1.0
F27 A:Y4Z901 2.2 54.9 1.0
O25 A:Y4Z901 2.3 44.1 1.0
C20 A:Y4Z901 2.8 40.5 1.0
C19 A:Y4Z901 3.1 39.0 1.0
CD1 A:ILE167 3.4 23.8 1.0
CG2 A:ILE167 3.5 20.6 1.0
CE2 A:PHE273 3.7 33.0 1.0
C21 A:Y4Z901 3.8 37.4 1.0
CD2 A:PHE273 3.9 30.1 1.0
CB A:ILE167 4.0 21.6 1.0
CG1 A:ILE167 4.1 21.2 1.0
C18 A:Y4Z901 4.3 41.4 1.0
CB A:ALA304 4.6 23.0 1.0
C16 A:Y4Z901 4.8 33.1 1.0
SD A:MET512 4.8 22.3 1.0
CE A:MET512 4.9 19.3 1.0
CZ A:PHE273 4.9 30.8 1.0

Fluorine binding site 3 out of 3 in 7g6d

Go back to Fluorine Binding Sites List in 7g6d
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 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 10-[[3- (Trifluoromethoxy)Phenyl]Methyl]-1,3,4,5-Tetrahydroazepino[3,4- B]Indole-2-Carboxamide, I.E. Smiles N1(C2C(CCCC2)C2=C1CN(CCC2)C(=O) N)CC1CCCC(C1)Oc(F)(F)F with IC50=0.35326 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:43.1
occ:1.00
 F29 A:Y4Z901 0.0 43.1 1.0
C26 A:Y4Z901 1.3 50.2 1.0
F27 A:Y4Z901 2.1 54.9 1.0
F28 A:Y4Z901 2.1 41.5 1.0
O25 A:Y4Z901 2.2 44.1 1.0
N A:ALA217 3.3 17.5 1.0
C A:LEU216 3.4 18.6 1.0
CB A:LEU216 3.4 20.0 1.0
CA A:ALA217 3.4 18.6 1.0
C20 A:Y4Z901 3.5 40.5 1.0
O A:LEU216 3.7 18.1 1.0
CB A:ALA217 3.9 18.0 1.0
CE A:MET512 4.0 19.3 1.0
CA A:LEU216 4.0 18.5 1.0
O A:LEU213 4.1 18.4 1.0
C21 A:Y4Z901 4.4 37.4 1.0
C19 A:Y4Z901 4.4 39.0 1.0
CG A:LEU216 4.6 24.8 1.0
SD A:MET512 4.7 22.3 1.0
C A:ALA217 4.8 18.4 1.0
CD1 A:ILE167 4.8 23.8 1.0
CD1 A:LEU216 4.8 27.4 1.0
CE2 A:PHE273 5.0 33.0 1.0
CG2 A:ILE167 5.0 20.6 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 18:05:15 2025

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