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Fluorine in PDB 7g2y: Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm, PDB code: 7g2y 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) 48.68 / 1.68
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.882, 91.634, 119.543, 90, 90, 90
R / Rfree (%) 17.9 / 22

Other elements in 7g2y:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm (pdb code 7g2y). 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm, PDB code: 7g2y:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g2y

Go back to Fluorine Binding Sites List in 7g2y
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:27.0
occ:1.00
 F17 A:XH0904 0.0 27.0 1.0
C16 A:XH0904 1.3 25.4 1.0
F18 A:XH0904 2.1 29.0 1.0
F19 A:XH0904 2.1 25.7 1.0
C15 A:XH0904 2.3 24.0 1.0
C14 A:XH0904 2.8 23.5 1.0
C20 A:XH0904 3.5 21.4 1.0
CB A:LEU216 3.5 18.4 1.0
CD1 A:LEU216 3.7 20.8 1.0
CG2 A:ILE167 4.1 19.6 1.0
C13 A:XH0904 4.2 24.9 1.0
CG A:LEU216 4.2 19.4 1.0
CB A:SER169 4.4 20.6 1.0
O A:LEU213 4.4 18.4 1.0
CD2 A:LEU213 4.5 20.0 1.0
C21 A:XH0904 4.7 22.0 1.0
CA A:LEU216 4.8 17.1 1.0
CG1 A:VAL356 4.8 17.2 1.0
OG A:SER169 4.8 24.0 1.0
C A:LEU216 4.8 17.4 1.0
N A:ALA217 4.9 17.5 1.0
CD2 A:LEU216 4.9 20.5 1.0
C12 A:XH0904 5.0 25.1 1.0

Fluorine binding site 2 out of 3 in 7g2y

Go back to Fluorine Binding Sites List in 7g2y
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:29.0
occ:1.00
 F18 A:XH0904 0.0 29.0 1.0
C16 A:XH0904 1.3 25.4 1.0
F17 A:XH0904 2.1 27.0 1.0
F19 A:XH0904 2.1 25.7 1.0
C15 A:XH0904 2.3 24.0 1.0
C14 A:XH0904 3.0 23.5 1.0
C20 A:XH0904 3.3 21.4 1.0
CD1 A:ILE167 3.6 18.8 1.0
CE2 A:PHE273 3.6 21.8 1.0
CG2 A:ILE167 3.7 19.6 1.0
CD2 A:PHE273 3.8 20.5 1.0
C13 A:XH0904 4.2 24.9 1.0
CB A:ILE167 4.3 17.8 1.0
CG1 A:ILE167 4.5 17.6 1.0
C21 A:XH0904 4.5 22.0 1.0
CB A:ALA304 4.6 23.0 1.0
C12 A:XH0904 4.9 25.1 1.0
CB A:LEU216 4.9 18.4 1.0
CZ A:PHE273 4.9 22.3 1.0

Fluorine binding site 3 out of 3 in 7g2y

Go back to Fluorine Binding Sites List in 7g2y
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 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 2-[(R)-2-[1-[3-[2- [(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfinyl]-1,3-Thiazole-5- Sulfonamide, I.E. Smiles C1(=Nc=C(S(=O)(=O)N)S1)[S@](=O) Cc[C@H]1CCN(C(=O)CCC2CCC(C(F)(F)F)CC2CN2N=Nc(=N2)C)CC1 with IC50=0.00230987 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:25.7
occ:1.00
 F19 A:XH0904 0.0 25.7 1.0
C16 A:XH0904 1.3 25.4 1.0
F18 A:XH0904 2.1 29.0 1.0
F17 A:XH0904 2.1 27.0 1.0
C15 A:XH0904 2.3 24.0 1.0
C20 A:XH0904 2.7 21.4 1.0
N A:ALA217 3.3 17.5 1.0
O A:LEU213 3.3 18.4 1.0
CB A:ALA217 3.5 19.1 1.0
CB A:LEU216 3.5 18.4 1.0
CA A:ALA217 3.5 18.3 1.0
C14 A:XH0904 3.6 23.5 1.0
C A:LEU216 3.6 17.4 1.0
C21 A:XH0904 4.1 22.0 1.0
CA A:LEU216 4.1 17.1 1.0
O A:LEU216 4.3 17.3 1.0
C A:LEU213 4.3 15.6 1.0
C13 A:XH0904 4.7 24.9 1.0
CD2 A:PHE273 4.7 20.5 1.0
CG A:LEU216 4.8 19.4 1.0
CA A:LEU213 4.8 16.8 1.0
CE2 A:PHE273 4.8 21.8 1.0
CD1 A:LEU216 4.8 20.8 1.0
N A:LEU216 4.9 15.4 1.0
C12 A:XH0904 4.9 25.1 1.0
C A:ALA217 5.0 19.7 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 17:51:54 2025

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