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Fluorine in PDB 7g2n: Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm, PDB code: 7g2n was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.61 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.952, 91.409, 119.249, 90, 90, 90
R / Rfree (%) 19.9 / 25.9

Other elements in 7g2n:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm (pdb code 7g2n). 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 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm, PDB code: 7g2n:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g2n

Go back to Fluorine Binding Sites List in 7g2n
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 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 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:80.0
occ:1.00
 F10 A:XVW907 0.0 80.0 1.0
C9 A:XVW907 1.3 80.0 1.0
C8 A:XVW907 2.3 80.0 1.0
C11 A:XVW907 2.4 80.0 1.0
CD2 A:LEU78 3.0 80.0 1.0
S7 A:XVW907 3.2 80.0 1.0
C19 A:XVW907 3.3 69.5 1.0
N18 A:XVW907 3.6 80.0 1.0
C6 A:XVW907 3.7 72.2 1.0
C12 A:XVW907 3.7 80.0 1.0
CE1 A:PHE249 3.8 80.0 1.0
CD2 A:PHE274 3.8 57.8 1.0
C17 A:XVW907 4.1 80.0 1.0
CG A:LEU78 4.2 80.0 1.0
CB A:PHE274 4.3 55.6 1.0
CD1 A:LEU78 4.3 80.0 1.0
CG A:PHE274 4.3 59.0 1.0
CD1 A:PHE249 4.5 80.0 1.0
CE2 A:PHE274 4.6 62.7 1.0
C5 A:XVW907 4.7 66.7 1.0
CZ A:PHE249 4.7 80.0 1.0
C20 A:XVW907 4.8 61.2 1.0
OG A:SER81 4.9 75.2 1.0
CE A:LYS248 4.9 80.0 1.0

Fluorine binding site 2 out of 4 in 7g2n

Go back to Fluorine Binding Sites List in 7g2n
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 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 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:47.1
occ:1.00
 F37 A:XVW907 0.0 47.1 1.0
C36 A:XVW907 1.3 44.2 1.0
F39 A:XVW907 2.2 50.1 1.0
F38 A:XVW907 2.2 41.5 1.0
C26 A:XVW907 2.4 44.9 1.0
C27 A:XVW907 2.7 45.9 1.0
O A:LEU213 3.1 40.6 1.0
N A:ALA217 3.2 36.2 1.0
CA A:ALA217 3.4 37.0 1.0
CB A:ALA217 3.5 38.5 1.0
CB A:LEU216 3.5 35.9 1.0
C A:LEU216 3.6 37.0 1.0
C25 A:XVW907 3.7 47.7 1.0
C28 A:XVW907 4.2 49.8 1.0
CA A:LEU216 4.2 34.9 1.0
O A:LEU216 4.2 38.0 1.0
C A:LEU213 4.2 36.4 1.0
CD1 A:LEU216 4.7 37.9 1.0
CG A:LEU216 4.8 36.7 1.0
C24 A:XVW907 4.8 47.2 1.0
CA A:LEU213 4.8 37.6 1.0
CD2 A:PHE273 4.8 50.1 1.0
N31 A:XVW907 4.8 53.9 1.0
N A:LEU216 4.8 34.6 1.0
C A:ALA217 4.9 37.6 1.0
CE2 A:PHE273 5.0 49.5 1.0
CZ3 A:TRP260 5.0 41.2 1.0

Fluorine binding site 3 out of 4 in 7g2n

Go back to Fluorine Binding Sites List in 7g2n
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 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 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:41.5
occ:1.00
 F38 A:XVW907 0.0 41.5 1.0
C36 A:XVW907 1.3 44.2 1.0
F39 A:XVW907 2.0 50.1 1.0
F37 A:XVW907 2.2 47.1 1.0
C26 A:XVW907 2.4 44.9 1.0
C25 A:XVW907 2.9 47.7 1.0
CD1 A:LEU216 3.5 37.9 1.0
C27 A:XVW907 3.5 45.9 1.0
CB A:LEU216 3.5 35.9 1.0
CG2 A:ILE167 4.1 41.2 1.0
CG A:LEU216 4.2 36.7 1.0
O A:LEU213 4.2 40.6 1.0
C24 A:XVW907 4.2 47.2 1.0
CD2 A:LEU213 4.4 37.8 1.0
CB A:SER169 4.5 41.2 1.0
CG1 A:VAL356 4.7 35.5 1.0
C28 A:XVW907 4.7 49.8 1.0
C A:LEU216 4.8 37.0 1.0
CA A:LEU216 4.8 34.9 1.0
N A:ALA217 4.8 36.2 1.0
CD2 A:LEU216 4.9 38.2 1.0
OG A:SER169 5.0 44.5 1.0

Fluorine binding site 4 out of 4 in 7g2n

Go back to Fluorine Binding Sites List in 7g2n
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 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 5-Fluoro-6-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylpyridine-3-Sulfonamide, I.E. Smiles O=C(N1CC[C@@H](SC2C(F)Cc(S(=O)(=O)N)CN2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00881095 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:50.1
occ:1.00
 F39 A:XVW907 0.0 50.1 1.0
C36 A:XVW907 1.3 44.2 1.0
F38 A:XVW907 2.0 41.5 1.0
F37 A:XVW907 2.2 47.1 1.0
C26 A:XVW907 2.4 44.9 1.0
C25 A:XVW907 3.0 47.7 1.0
C27 A:XVW907 3.4 45.9 1.0
CG2 A:ILE167 3.5 41.2 1.0
CE2 A:PHE273 3.8 49.5 1.0
CD2 A:PHE273 3.9 50.1 1.0
CD1 A:ILE167 4.0 41.8 1.0
C24 A:XVW907 4.3 47.2 1.0
CB A:ILE167 4.3 40.6 1.0
C28 A:XVW907 4.6 49.8 1.0
CG1 A:ILE167 4.6 40.6 1.0
CB A:LEU216 4.8 35.9 1.0
C23 A:XVW907 4.9 49.6 1.0
N A:ALA217 5.0 36.2 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 17:50:16 2025

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