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Fluorine in PDB 7g30: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm, PDB code: 7g30 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) 46.08 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.091, 92.158, 120.803, 90, 90, 90
R / Rfree (%) 19 / 22.8

Other elements in 7g30:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm (pdb code 7g30). 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-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm, PDB code: 7g30:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g30

Go back to Fluorine Binding Sites List in 7g30
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 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-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:44.9
occ:1.00
 F3 A:XDB904 0.0 44.9 1.0
C2 A:XDB904 1.3 40.3 1.0
C4 A:XDB904 2.3 41.5 1.0
C1 A:XDB904 2.4 39.8 1.0
S12 A:XDB904 2.8 45.1 1.0
CD A:LYS248 3.3 40.7 1.0
CZ2 A:TRP254 3.4 26.3 1.0
CG A:LYS248 3.5 40.4 1.0
O A:LYS248 3.5 37.9 1.0
CE A:LYS248 3.6 48.5 1.0
C5 A:XDB904 3.6 46.9 1.0
CE2 A:PHE210 3.6 37.9 1.0
C11 A:XDB904 3.6 41.3 1.0
CB A:LYS248 3.8 33.0 1.0
CH2 A:TRP254 3.9 28.9 1.0
C A:LYS248 4.0 37.2 1.0
C10 A:XDB904 4.1 40.7 1.0
CZ A:PHE210 4.3 36.2 1.0
CD1 A:PHE249 4.4 44.0 1.0
CE2 A:TRP254 4.4 28.2 1.0
CE1 A:PHE249 4.5 47.1 1.0
CA A:LYS248 4.5 38.4 1.0
CD2 A:PHE210 4.6 33.4 1.0
C13 A:XDB904 4.6 46.5 1.0
N A:PHE249 4.6 40.4 1.0
NZ A:LYS248 4.8 53.7 1.0
NE1 A:TRP254 4.9 30.8 1.0
CZ A:PHE241 4.9 31.3 1.0
S6 A:XDB904 4.9 57.0 1.0
CA A:PHE249 5.0 39.1 1.0

Fluorine binding site 2 out of 4 in 7g30

Go back to Fluorine Binding Sites List in 7g30
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 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-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:32.4
occ:1.00
 F37 A:XDB904 0.0 32.4 1.0
C36 A:XDB904 1.3 31.1 1.0
F38 A:XDB904 2.0 29.6 1.0
F39 A:XDB904 2.1 32.2 1.0
C26 A:XDB904 2.4 28.1 1.0
C25 A:XDB904 3.0 28.6 1.0
C27 A:XDB904 3.5 30.1 1.0
CB A:LEU216 3.6 22.2 1.0
CD1 A:LEU216 3.7 25.4 1.0
CG2 A:ILE167 4.0 22.5 1.0
CG A:LEU216 4.2 24.8 1.0
C24 A:XDB904 4.3 28.0 1.0
CB A:SER169 4.5 24.9 1.0
O A:LEU213 4.5 20.4 1.0
CD2 A:LEU213 4.6 24.0 1.0
C28 A:XDB904 4.7 31.5 1.0
C A:LEU216 4.8 22.2 1.0
CA A:LEU216 4.8 21.2 1.0
CG1 A:VAL356 4.8 23.3 1.0
N A:ALA217 4.9 19.8 1.0
OG A:SER169 4.9 27.7 1.0
CD2 A:LEU216 4.9 29.4 1.0

Fluorine binding site 3 out of 4 in 7g30

Go back to Fluorine Binding Sites List in 7g30
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 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-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:29.6
occ:1.00
 F38 A:XDB904 0.0 29.6 1.0
C36 A:XDB904 1.3 31.1 1.0
F37 A:XDB904 2.0 32.4 1.0
F39 A:XDB904 2.1 32.2 1.0
C26 A:XDB904 2.4 28.1 1.0
C25 A:XDB904 3.0 28.6 1.0
C27 A:XDB904 3.4 30.1 1.0
CD1 A:ILE167 3.6 26.6 1.0
CG2 A:ILE167 3.7 22.5 1.0
CE2 A:PHE273 3.7 27.4 1.0
CD2 A:PHE273 3.9 24.1 1.0
CB A:ILE167 4.2 23.4 1.0
C24 A:XDB904 4.3 28.0 1.0
CG1 A:ILE167 4.4 22.9 1.0
C28 A:XDB904 4.6 31.5 1.0
CB A:ALA304 4.7 23.2 1.0
CB A:LEU216 4.9 22.2 1.0
C23 A:XDB904 4.9 29.9 1.0
CZ A:PHE273 4.9 26.0 1.0

Fluorine binding site 4 out of 4 in 7g30

Go back to Fluorine Binding Sites List in 7g30
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 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-[[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Methylsulfanyl]Benzenesulfonamide, I.E. Smiles C1(C(F)Cc(S(=O)(=O)N)CC1)Sc[C@H]1CCN(CC1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.0105744 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F904

b:32.2
occ:1.00
 F39 A:XDB904 0.0 32.2 1.0
C36 A:XDB904 1.3 31.1 1.0
F38 A:XDB904 2.1 29.6 1.0
F37 A:XDB904 2.1 32.4 1.0
C26 A:XDB904 2.4 28.1 1.0
C27 A:XDB904 2.7 30.1 1.0
N A:ALA217 3.3 19.8 1.0
O A:LEU213 3.4 20.4 1.0
CB A:ALA217 3.4 21.8 1.0
CA A:ALA217 3.5 21.2 1.0
CB A:LEU216 3.6 22.2 1.0
C25 A:XDB904 3.6 28.6 1.0
C A:LEU216 3.7 22.2 1.0
C28 A:XDB904 4.1 31.5 1.0
CA A:LEU216 4.3 21.2 1.0
O A:LEU216 4.3 21.5 1.0
C A:LEU213 4.4 21.4 1.0
CD2 A:PHE273 4.7 24.1 1.0
C24 A:XDB904 4.7 28.0 1.0
CE2 A:PHE273 4.8 27.4 1.0
N31 A:XDB904 4.8 37.5 1.0
CG A:LEU216 4.8 24.8 1.0
CD1 A:LEU216 4.8 25.4 1.0
C29 A:XDB904 4.9 34.8 1.0
CA A:LEU213 4.9 22.5 1.0
C23 A:XDB904 4.9 29.9 1.0
CZ3 A:TRP260 5.0 26.8 1.0
C A:ALA217 5.0 21.1 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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