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Fluorine in PDB 7g5q: Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm, PDB code: 7g5q was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.045, 92.177, 119.482, 90, 90, 90
R / Rfree (%) 19 / 22.4

Other elements in 7g5q:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm (pdb code 7g5q). 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm, PDB code: 7g5q:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g5q

Go back to Fluorine Binding Sites List in 7g5q
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:22.7
occ:1.00
 F9 A:Y8Q903 0.0 22.7 1.0
C8 A:Y8Q903 1.3 24.3 1.0
F11 A:Y8Q903 2.1 27.1 1.0
F10 A:Y8Q903 2.1 27.4 1.0
C5 A:Y8Q903 2.4 20.3 1.0
C4 A:Y8Q903 2.8 18.4 1.0
CE2 A:PHE274 3.4 18.3 1.0
CE2 A:PHE210 3.5 17.8 1.0
C29 A:Y8Q903 3.5 13.3 1.0
C6 A:Y8Q903 3.6 19.7 1.0
CH2 A:TRP254 3.7 15.5 1.0
CD2 A:PHE274 3.8 17.5 1.0
CZ A:PHE210 3.9 16.9 1.0
CZ2 A:TRP254 3.9 14.1 1.0
S A:DMS904 4.0 31.7 1.0
O28 A:Y8Q903 4.0 12.8 1.0
C3 A:Y8Q903 4.1 17.5 1.0
CD2 A:PHE210 4.4 15.8 1.0
CZ A:PHE274 4.4 17.5 1.0
C2 A:DMS904 4.5 29.1 1.0
C1 A:DMS904 4.6 27.0 1.0
CZ3 A:TRP254 4.7 15.3 1.0
C1 A:Y8Q903 4.8 19.2 1.0
C23 A:Y8Q903 4.9 13.1 1.0
C2 A:Y8Q903 5.0 20.9 1.0
CE1 A:PHE210 5.0 16.3 1.0

Fluorine binding site 2 out of 3 in 7g5q

Go back to Fluorine Binding Sites List in 7g5q
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:27.4
occ:1.00
 F10 A:Y8Q903 0.0 27.4 1.0
C8 A:Y8Q903 1.3 24.3 1.0
F11 A:Y8Q903 2.1 27.1 1.0
F9 A:Y8Q903 2.1 22.7 1.0
C5 A:Y8Q903 2.3 20.3 1.0
C6 A:Y8Q903 2.8 19.7 1.0
C2 A:DMS904 3.4 29.1 1.0
S A:DMS904 3.5 31.7 1.0
C4 A:Y8Q903 3.5 18.4 1.0
CE1 A:PHE249 3.6 29.6 1.0
C1 A:DMS904 3.7 27.0 1.0
CD1 A:PHE249 3.9 30.3 1.0
C1 A:Y8Q903 4.1 19.2 1.0
CD2 A:PHE274 4.2 17.5 1.0
CE2 A:PHE274 4.3 18.3 1.0
CE A:LYS248 4.7 20.0 1.0
C3 A:Y8Q903 4.7 17.5 1.0
CZ A:PHE249 4.7 29.8 1.0
CD1 A:LEU78 4.8 22.1 1.0
CZ2 A:TRP254 4.8 14.1 1.0
CG A:PHE274 4.9 16.1 1.0
C2 A:Y8Q903 4.9 20.9 1.0
O A:DMS904 5.0 30.3 1.0

Fluorine binding site 3 out of 3 in 7g5q

Go back to Fluorine Binding Sites List in 7g5q
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 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 (3S)-3-[[2-[2- Methoxy-6-[[Methyl-[(4-Methyl-1,3-Thiazol-2-Yl) Methyl]Amino]Methyl]Phenoxy]Acetyl]Amino]-N-Methyl-3-[3- (Trifluoromethyl)Phenyl]Propanamide, I.E. Smiles C1CC(Cc(C1)C(F)(F) F)[C@H](Cc(=O)Nc)Nc(=O)COC1C(CCCC1CN(CC1=Nc(=CS1)C)C)Oc with IC50=0.814833 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F903

b:27.1
occ:1.00
 F11 A:Y8Q903 0.0 27.1 1.0
C8 A:Y8Q903 1.4 24.3 1.0
F9 A:Y8Q903 2.1 22.7 1.0
F10 A:Y8Q903 2.1 27.4 1.0
C5 A:Y8Q903 2.4 20.3 1.0
CE A:LYS248 3.0 20.0 1.0
C6 A:Y8Q903 3.1 19.7 1.0
CD A:LYS248 3.2 18.3 1.0
C4 A:Y8Q903 3.3 18.4 1.0
CE2 A:PHE210 3.4 17.8 1.0
CZ A:PHE210 3.7 16.9 1.0
CG A:LYS248 3.9 18.1 1.0
CE1 A:PHE249 4.3 29.6 1.0
C1 A:Y8Q903 4.4 19.2 1.0
NZ A:LYS248 4.5 21.5 1.0
C3 A:Y8Q903 4.5 17.5 1.0
CZ2 A:TRP254 4.5 14.1 1.0
CB A:LYS248 4.6 18.9 1.0
CD2 A:PHE210 4.6 15.8 1.0
CD1 A:PHE249 4.7 30.3 1.0
CH2 A:TRP254 4.8 15.5 1.0
CZ A:PHE249 4.9 29.8 1.0
O A:LYS248 5.0 18.7 1.0
C2 A:Y8Q903 5.0 20.9 1.0
C1 A:DMS904 5.0 27.0 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 17:58:12 2025

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