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Fluorine in PDB 7g2h: 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm, PDB code: 7g2h 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) 48.44 / 2.54
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.802, 91.466, 118.707, 90, 90, 90
R / Rfree (%) 18.9 / 25.7

Other elements in 7g2h:

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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm also contains other interesting chemical elements:

Zinc (Zn) 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm (pdb code 7g2h). 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm, PDB code: 7g2h:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g2h

Go back to Fluorine Binding Sites List in 7g2h
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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:80.0
occ:1.00
 F10 A:XTO901 0.0 80.0 1.0
C9 A:XTO901 1.3 80.0 1.0
C8 A:XTO901 2.3 80.0 1.0
C11 A:XTO901 2.4 80.0 1.0
O19 A:XTO901 2.6 80.0 1.0
S7 A:XTO901 3.0 80.0 1.0
CD2 A:LEU78 3.1 76.1 1.0
CE1 A:PHE249 3.4 80.0 1.0
CD1 A:LEU78 3.5 77.1 1.0
C18 A:XTO901 3.6 80.0 1.0
C12 A:XTO901 3.7 80.0 1.0
CG A:LEU78 3.9 77.2 1.0
CD1 A:PHE249 4.0 80.0 1.0
C6 A:XTO901 4.0 80.0 1.0
C21 A:XTO901 4.0 80.0 1.0
C17 A:XTO901 4.1 80.0 1.0
O20 A:XTO901 4.2 80.0 1.0
CD2 A:PHE274 4.3 57.8 1.0
CZ A:PHE249 4.5 80.0 1.0
CE1 A:TYR82 4.6 80.0 1.0
CG A:PHE274 4.6 60.9 1.0
CB A:PHE274 4.7 57.6 1.0
OH A:TYR82 4.7 80.0 1.0
C5 A:XTO901 4.8 78.0 1.0
OG A:SER81 4.9 80.0 1.0
CE2 A:PHE274 4.9 54.5 1.0
CB A:SER81 4.9 80.0 1.0
CB A:LEU78 5.0 76.0 1.0

Fluorine binding site 2 out of 4 in 7g2h

Go back to Fluorine Binding Sites List in 7g2h
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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:58.3
occ:1.00
 F39 A:XTO901 0.0 58.3 1.0
C38 A:XTO901 1.3 56.1 1.0
F41 A:XTO901 2.1 55.1 1.0
F40 A:XTO901 2.1 50.4 1.0
C28 A:XTO901 2.4 56.9 1.0
C27 A:XTO901 3.1 52.7 1.0
C29 A:XTO901 3.5 56.6 1.0
CE2 A:PHE273 3.7 53.2 1.0
CG2 A:ILE167 3.8 39.5 1.0
CD1 A:ILE167 3.8 39.1 1.0
CD2 A:PHE273 3.9 53.2 1.0
C26 A:XTO901 4.4 52.4 1.0
CB A:ILE167 4.5 36.5 1.0
C30 A:XTO901 4.6 56.2 1.0
CG1 A:ILE167 4.7 36.9 1.0
CB A:LEU216 4.7 39.8 1.0
CE A:MET512 4.8 45.3 1.0
N A:ALA217 4.9 39.6 1.0
CA A:ALA217 4.9 38.4 1.0
CZ A:PHE273 4.9 50.5 1.0
CB A:ALA304 5.0 53.0 1.0
CB A:ALA217 5.0 42.0 1.0

Fluorine binding site 3 out of 4 in 7g2h

Go back to Fluorine Binding Sites List in 7g2h
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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:50.4
occ:1.00
 F40 A:XTO901 0.0 50.4 1.0
C38 A:XTO901 1.3 56.1 1.0
F39 A:XTO901 2.1 58.3 1.0
F41 A:XTO901 2.2 55.1 1.0
C28 A:XTO901 2.4 56.9 1.0
C29 A:XTO901 2.8 56.6 1.0
O A:LEU213 3.1 35.8 1.0
N A:ALA217 3.2 39.6 1.0
CB A:LEU216 3.4 39.8 1.0
CB A:ALA217 3.5 42.0 1.0
CA A:ALA217 3.5 38.4 1.0
C27 A:XTO901 3.6 52.7 1.0
C A:LEU216 3.7 41.7 1.0
CA A:LEU216 4.1 39.5 1.0
C30 A:XTO901 4.2 56.2 1.0
C A:LEU213 4.2 37.7 1.0
O A:LEU216 4.3 42.9 1.0
CD1 A:LEU216 4.6 42.4 1.0
CG A:LEU216 4.6 42.0 1.0
CA A:LEU213 4.7 40.2 1.0
C26 A:XTO901 4.8 52.4 1.0
N A:LEU216 4.9 36.1 1.0
CD2 A:PHE273 4.9 53.2 1.0
CE2 A:PHE273 5.0 53.2 1.0

Fluorine binding site 4 out of 4 in 7g2h

Go back to Fluorine Binding Sites List in 7g2h
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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 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]Sulfonylbenzenesulfonamide, I.E. Smiles O=C(N1CC[C@@H](S(=O)(=O)C2C(F)Cc(S(=O)(=O)N)CC2)CC1) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F with IC50=0.00379624 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:55.1
occ:1.00
 F41 A:XTO901 0.0 55.1 1.0
C38 A:XTO901 1.3 56.1 1.0
F39 A:XTO901 2.1 58.3 1.0
F40 A:XTO901 2.2 50.4 1.0
C28 A:XTO901 2.4 56.9 1.0
C27 A:XTO901 2.8 52.7 1.0
C29 A:XTO901 3.5 56.6 1.0
CD1 A:LEU216 3.7 42.4 1.0
CB A:LEU216 3.7 39.8 1.0
CG2 A:ILE167 4.1 39.5 1.0
C26 A:XTO901 4.1 52.4 1.0
CG A:LEU216 4.3 42.0 1.0
CB A:SER169 4.3 43.1 1.0
O A:LEU213 4.5 35.8 1.0
CD2 A:LEU213 4.5 43.7 1.0
OG A:SER169 4.6 48.2 1.0
C30 A:XTO901 4.7 56.2 1.0
CG1 A:VAL356 4.8 46.7 1.0
C25 A:XTO901 4.9 53.9 1.0
CA A:LEU216 5.0 39.5 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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