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Fluorine in PDB 7g2i: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm, PDB code: 7g2i 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) 48.39 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.539, 91.509, 118.741, 90, 90, 90
R / Rfree (%) 15.9 / 18.5

Other elements in 7g2i:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms
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 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm (pdb code 7g2i). 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 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm, PDB code: 7g2i:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g2i

Go back to Fluorine Binding Sites List in 7g2i
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 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 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F912

b:22.9
occ:1.00
 F27 A:XTU912 0.0 22.9 1.0
C26 A:XTU912 1.3 20.5 1.0
F29 A:XTU912 2.0 22.0 1.0
F28 A:XTU912 2.1 19.1 1.0
C25 A:XTU912 2.3 17.2 1.0
C30 A:XTU912 3.0 19.3 1.0
C24 A:XTU912 3.3 17.5 1.0
CD1 A:ILE167 3.7 17.2 1.0
CG2 A:ILE167 3.7 15.8 1.0
CE2 A:PHE273 3.7 19.1 1.0
CD2 A:PHE273 3.9 18.4 1.0
C31 A:XTU912 4.3 18.9 1.0
CB A:ILE167 4.3 15.6 1.0
CG1 A:ILE167 4.5 15.7 1.0
C16 A:XTU912 4.5 18.1 1.0
CB A:LEU216 4.8 14.3 1.0
CE A:MET512 4.8 17.4 1.0
CB A:ALA304 4.8 17.5 1.0
C15 A:XTU912 4.9 18.9 1.0
CZ A:PHE273 4.9 19.8 1.0
CA A:ALA217 4.9 14.4 1.0
N A:ALA217 4.9 13.5 1.0
SD A:MET512 5.0 17.3 1.0

Fluorine binding site 2 out of 4 in 7g2i

Go back to Fluorine Binding Sites List in 7g2i
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 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 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F912

b:19.1
occ:1.00
 F28 A:XTU912 0.0 19.1 1.0
C26 A:XTU912 1.3 20.5 1.0
F27 A:XTU912 2.1 22.9 1.0
F29 A:XTU912 2.1 22.0 1.0
C25 A:XTU912 2.4 17.2 1.0
C24 A:XTU912 2.8 17.5 1.0
N A:ALA217 3.2 13.5 1.0
O A:LEU213 3.3 14.6 1.0
CA A:ALA217 3.4 14.4 1.0
CB A:LEU216 3.5 14.3 1.0
CB A:ALA217 3.5 15.6 1.0
C A:LEU216 3.6 14.1 1.0
C30 A:XTU912 3.6 19.3 1.0
CA A:LEU216 4.1 14.2 1.0
C16 A:XTU912 4.2 18.1 1.0
O A:LEU216 4.2 14.7 1.0
C A:LEU213 4.4 13.4 1.0
CG A:LEU216 4.7 14.9 1.0
CD1 A:LEU216 4.8 16.6 1.0
C31 A:XTU912 4.8 18.9 1.0
N A:LEU216 4.8 13.5 1.0
CA A:LEU213 4.9 13.9 1.0
CD2 A:PHE273 4.9 18.4 1.0
C A:ALA217 4.9 14.7 1.0
CE2 A:PHE273 4.9 19.1 1.0
C15 A:XTU912 5.0 18.9 1.0

Fluorine binding site 3 out of 4 in 7g2i

Go back to Fluorine Binding Sites List in 7g2i
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 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 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F912

b:22.0
occ:1.00
 F29 A:XTU912 0.0 22.0 1.0
C26 A:XTU912 1.3 20.5 1.0
F27 A:XTU912 2.0 22.9 1.0
F28 A:XTU912 2.1 19.1 1.0
C25 A:XTU912 2.4 17.2 1.0
C30 A:XTU912 2.8 19.3 1.0
C24 A:XTU912 3.5 17.5 1.0
CB A:LEU216 3.6 14.3 1.0
CD1 A:LEU216 3.7 16.6 1.0
CG2 A:ILE167 4.0 15.8 1.0
C31 A:XTU912 4.2 18.9 1.0
CG A:LEU216 4.2 14.9 1.0
O A:LEU213 4.5 14.6 1.0
CB A:SER169 4.6 17.8 1.0
CD2 A:LEU213 4.6 17.4 1.0
CG1 A:VAL356 4.7 15.4 1.0
C16 A:XTU912 4.7 18.1 1.0
CA A:LEU216 4.8 14.2 1.0
C A:LEU216 4.8 14.1 1.0
N A:ALA217 4.8 13.5 1.0
CD2 A:LEU216 4.9 16.6 1.0
C15 A:XTU912 5.0 18.9 1.0
OG A:SER169 5.0 18.6 1.0

Fluorine binding site 4 out of 4 in 7g2i

Go back to Fluorine Binding Sites List in 7g2i
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 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 3-Fluoro-4-[2-[1- [3-[2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Ethylsulfonyl]Benzenesulfonamide, I.E. Smiles C1(S(=O)(=O)Cc[C@H]2CCN(C(=O)CCC3C(CN4N=C(C)N=N4)Cc(C(F) (F)F)CC3)CC2)Ccc(S(=O)(=O)N)CC1F with IC50=0.00184303 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F912

b:69.4
occ:1.00
 F43 A:XTU912 0.0 69.4 1.0
C42 A:XTU912 1.3 67.5 1.0
C1 A:XTU912 2.3 62.5 1.0
C41 A:XTU912 2.3 66.2 1.0
O4 A:XTU912 3.0 64.6 1.0
S2 A:XTU912 3.0 68.9 1.0
C5 A:XTU912 3.0 54.1 1.0
CE1 A:PHE249 3.3 46.4 1.0
CD2 A:LEU78 3.4 33.0 1.0
CD1 A:LEU78 3.5 38.3 1.0
C34 A:XTU912 3.5 63.6 1.0
C36 A:XTU912 3.5 71.3 1.0
CD1 A:PHE249 3.8 45.0 1.0
C35 A:XTU912 4.0 70.1 1.0
CE1 A:TYR82 4.0 52.8 1.0
CG A:LEU78 4.0 32.4 1.0
CB A:SER81 4.3 37.5 1.0
O3 A:XTU912 4.3 71.0 1.0
OH A:TYR82 4.4 58.2 1.0
CZ A:PHE249 4.5 48.1 1.0
C6 A:XTU912 4.5 42.0 1.0
OG A:SER81 4.6 35.1 1.0
CZ A:TYR82 4.6 52.9 1.0
CD1 A:TYR82 4.8 49.4 1.0
CB A:LEU78 4.9 30.4 1.0
S37 A:XTU912 5.0 78.5 1.0
C8 A:XTU912 5.0 30.1 1.0
CD2 A:PHE274 5.0 21.9 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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