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Fluorine in PDB 7g7z: 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]Sulfanylbenzoic Acid

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]Sulfanylbenzoic Acid

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]Sulfanylbenzoic Acid:
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]Sulfanylbenzoic Acid, PDB code: 7g7z 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) 48.97 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.096, 92.112, 120.482, 90, 90, 90
R / Rfree (%) 20.2 / 24.2

Other elements in 7g7z:

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]Sulfanylbenzoic Acid also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Calcium (Ca) 2 atoms
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-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid (pdb code 7g7z). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 7 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]Sulfanylbenzoic Acid, PDB code: 7g7z:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Fluorine binding site 1 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 1 out of 7 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]Sulfanylbenzoic Acid


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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:44.0
occ:0.70
 F1 A:Y1B907 0.0 44.0 0.7
C2 A:Y1B907 1.3 38.9 0.7
C7 A:Y1B907 2.2 38.0 0.7
C3 A:Y1B907 2.3 35.4 0.7
CE2 A:PHE210 2.9 35.0 1.0
S11 A:Y1B907 3.0 39.7 0.7
CZ A:PHE210 3.2 34.0 1.0
C6 A:Y1B907 3.4 38.5 0.7
C38 A:Y1B907 3.5 33.9 0.7
C4 A:Y1B907 3.5 41.2 0.7
CH2 A:TRP254 3.7 28.0 1.0
C12 A:Y1B907 3.8 34.0 0.7
CZ2 A:TRP254 3.9 28.0 1.0
CD2 A:PHE210 3.9 33.9 1.0
C5 A:Y1B907 4.0 38.6 0.7
CE2 A:PHE274 4.1 37.5 1.0
CD A:LYS248 4.2 44.3 1.0
CE1 A:PHE210 4.3 34.2 1.0
CE A:LYS248 4.3 46.4 1.0
C34 A:Y1B907 4.4 26.7 0.7
C34 A:Y1B907 4.4 32.3 0.3
C8 A:Y1B907 4.6 39.7 0.7
CD2 A:PHE274 4.6 35.3 1.0
C37 A:Y1B907 4.7 30.1 0.3
O10 A:Y1B907 4.8 39.8 0.7
CZ3 A:TRP254 4.9 27.1 1.0
C13 A:Y1B907 4.9 33.9 0.7
CG A:PHE210 4.9 28.7 1.0
C33 A:Y1B907 4.9 30.4 0.7
C33 A:Y1B907 4.9 34.1 0.3
CG A:LYS248 4.9 42.6 1.0
C37 A:Y1B907 4.9 31.4 0.7
C12 A:Y1B907 5.0 30.1 0.3

Fluorine binding site 2 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 2 out of 7 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]Sulfanylbenzoic Acid


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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:29.3
occ:0.70
 F24 A:Y1B907 0.0 29.3 0.7
F24 A:Y1B907 0.0 32.1 0.3
C23 A:Y1B907 1.3 31.6 0.3
C23 A:Y1B907 1.3 28.6 0.7
F26 A:Y1B907 2.0 31.6 0.3
F26 A:Y1B907 2.0 28.1 0.7
F25 A:Y1B907 2.1 31.0 0.3
F25 A:Y1B907 2.1 27.1 0.7
C22 A:Y1B907 2.4 30.4 0.3
C22 A:Y1B907 2.4 26.2 0.7
C21 A:Y1B907 3.0 29.9 0.3
C21 A:Y1B907 3.0 25.8 0.7
C27 A:Y1B907 3.3 30.0 0.3
C27 A:Y1B907 3.3 25.5 0.7
CG2 A:ILE167 3.6 23.2 1.0
CD1 A:ILE167 3.8 24.6 1.0
CE2 A:PHE273 3.8 30.3 1.0
CD2 A:PHE273 4.0 26.8 1.0
CB A:ILE167 4.3 23.1 1.0
C20 A:Y1B907 4.3 30.1 0.3
C20 A:Y1B907 4.3 26.2 0.7
C28 A:Y1B907 4.5 30.6 0.3
C28 A:Y1B907 4.5 26.5 0.7
CG1 A:ILE167 4.6 23.6 1.0
CB A:LEU216 4.7 21.6 1.0
N A:ALA217 4.9 21.8 1.0
CB A:ALA304 4.9 26.9 1.0
C19 A:Y1B907 4.9 30.0 0.3
CA A:ALA217 4.9 23.5 1.0
C19 A:Y1B907 4.9 26.1 0.7

Fluorine binding site 3 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 3 out of 7 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]Sulfanylbenzoic Acid


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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:32.1
occ:0.30
 F24 A:Y1B907 0.0 32.1 0.3
F24 A:Y1B907 0.0 29.3 0.7
C23 A:Y1B907 1.3 31.6 0.3
C23 A:Y1B907 1.3 28.6 0.7
F26 A:Y1B907 2.0 31.6 0.3
F26 A:Y1B907 2.0 28.1 0.7
F25 A:Y1B907 2.1 31.0 0.3
F25 A:Y1B907 2.1 27.1 0.7
C22 A:Y1B907 2.4 30.4 0.3
C22 A:Y1B907 2.4 26.2 0.7
C21 A:Y1B907 3.0 29.9 0.3
C21 A:Y1B907 3.1 25.8 0.7
C27 A:Y1B907 3.4 30.0 0.3
C27 A:Y1B907 3.4 25.5 0.7
CG2 A:ILE167 3.6 23.2 1.0
CD1 A:ILE167 3.8 24.6 1.0
CE2 A:PHE273 3.8 30.3 1.0
CD2 A:PHE273 4.0 26.8 1.0
CB A:ILE167 4.3 23.1 1.0
C20 A:Y1B907 4.3 30.1 0.3
C20 A:Y1B907 4.3 26.2 0.7
CG1 A:ILE167 4.6 23.6 1.0
C28 A:Y1B907 4.6 30.6 0.3
C28 A:Y1B907 4.6 26.5 0.7
CB A:LEU216 4.7 21.6 1.0
N A:ALA217 4.8 21.8 1.0
CB A:ALA304 4.9 26.9 1.0
CA A:ALA217 4.9 23.5 1.0
C19 A:Y1B907 4.9 30.0 0.3
C19 A:Y1B907 4.9 26.1 0.7
C A:LEU216 5.0 24.4 1.0

Fluorine binding site 4 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 4 out of 7 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]Sulfanylbenzoic Acid


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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:27.1
occ:0.70
 F25 A:Y1B907 0.0 27.1 0.7
F25 A:Y1B907 0.0 31.0 0.3
C23 A:Y1B907 1.3 28.6 0.7
C23 A:Y1B907 1.3 31.6 0.3
F26 A:Y1B907 2.1 28.1 0.7
F24 A:Y1B907 2.1 32.1 0.3
F24 A:Y1B907 2.1 29.3 0.7
F26 A:Y1B907 2.1 31.6 0.3
C22 A:Y1B907 2.4 30.4 0.3
C22 A:Y1B907 2.4 26.2 0.7
C27 A:Y1B907 2.7 25.5 0.7
C27 A:Y1B907 2.7 30.0 0.3
N A:ALA217 3.1 21.8 1.0
O A:LEU213 3.3 21.1 1.0
CA A:ALA217 3.4 23.5 1.0
CB A:ALA217 3.4 23.6 1.0
CB A:LEU216 3.5 21.6 1.0
C A:LEU216 3.6 24.4 1.0
C21 A:Y1B907 3.6 25.8 0.7
C21 A:Y1B907 3.6 29.9 0.3
CA A:LEU216 4.1 22.8 1.0
C28 A:Y1B907 4.1 26.5 0.7
C28 A:Y1B907 4.1 30.6 0.3
O A:LEU216 4.2 21.1 1.0
C A:LEU213 4.3 21.9 1.0
CG A:LEU216 4.7 23.2 1.0
C20 A:Y1B907 4.7 26.2 0.7
C20 A:Y1B907 4.7 30.1 0.3
CD1 A:LEU216 4.8 26.0 1.0
CD2 A:PHE273 4.8 26.8 1.0
CA A:LEU213 4.8 24.2 1.0
N A:LEU216 4.8 21.2 1.0
CE2 A:PHE273 4.8 30.3 1.0
C19 A:Y1B907 4.9 26.1 0.7
C19 A:Y1B907 5.0 30.0 0.3
C A:ALA217 5.0 23.5 1.0
C29 A:Y1B907 5.0 27.6 0.7
C29 A:Y1B907 5.0 31.8 0.3

Fluorine binding site 5 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 5 out of 7 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]Sulfanylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:31.0
occ:0.30
 F25 A:Y1B907 0.0 31.0 0.3
F25 A:Y1B907 0.0 27.1 0.7
C23 A:Y1B907 1.3 28.6 0.7
C23 A:Y1B907 1.3 31.6 0.3
F26 A:Y1B907 2.1 28.1 0.7
F26 A:Y1B907 2.1 31.6 0.3
F24 A:Y1B907 2.1 32.1 0.3
F24 A:Y1B907 2.1 29.3 0.7
C22 A:Y1B907 2.4 30.4 0.3
C22 A:Y1B907 2.4 26.2 0.7
C27 A:Y1B907 2.7 25.5 0.7
C27 A:Y1B907 2.7 30.0 0.3
N A:ALA217 3.1 21.8 1.0
O A:LEU213 3.3 21.1 1.0
CB A:LEU216 3.5 21.6 1.0
CA A:ALA217 3.5 23.5 1.0
CB A:ALA217 3.5 23.6 1.0
C A:LEU216 3.6 24.4 1.0
C21 A:Y1B907 3.6 25.8 0.7
C21 A:Y1B907 3.6 29.9 0.3
CA A:LEU216 4.1 22.8 1.0
C28 A:Y1B907 4.1 26.5 0.7
C28 A:Y1B907 4.1 30.6 0.3
O A:LEU216 4.2 21.1 1.0
C A:LEU213 4.4 21.9 1.0
CG A:LEU216 4.7 23.2 1.0
C20 A:Y1B907 4.7 26.2 0.7
C20 A:Y1B907 4.7 30.1 0.3
CD1 A:LEU216 4.8 26.0 1.0
CD2 A:PHE273 4.8 26.8 1.0
CA A:LEU213 4.8 24.2 1.0
N A:LEU216 4.8 21.2 1.0
CE2 A:PHE273 4.8 30.3 1.0
C19 A:Y1B907 4.9 26.1 0.7
C19 A:Y1B907 5.0 30.0 0.3
C A:ALA217 5.0 23.5 1.0
C29 A:Y1B907 5.0 27.6 0.7

Fluorine binding site 6 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 6 out of 7 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]Sulfanylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:28.1
occ:0.70
 F26 A:Y1B907 0.0 28.1 0.7
F26 A:Y1B907 0.0 31.6 0.3
C23 A:Y1B907 1.3 28.6 0.7
C23 A:Y1B907 1.3 31.6 0.3
F24 A:Y1B907 2.0 32.1 0.3
F24 A:Y1B907 2.0 29.3 0.7
F25 A:Y1B907 2.1 31.0 0.3
F25 A:Y1B907 2.1 27.1 0.7
C22 A:Y1B907 2.4 26.2 0.7
C22 A:Y1B907 2.4 30.4 0.3
C21 A:Y1B907 2.9 25.8 0.7
C21 A:Y1B907 3.0 29.9 0.3
CB A:LEU216 3.4 21.6 1.0
C27 A:Y1B907 3.5 25.5 0.7
C27 A:Y1B907 3.5 30.0 0.3
CD1 A:LEU216 3.6 26.0 1.0
CG A:LEU216 4.1 23.2 1.0
CG2 A:ILE167 4.1 23.2 1.0
C20 A:Y1B907 4.3 26.2 0.7
C20 A:Y1B907 4.3 30.1 0.3
O A:LEU213 4.3 21.1 1.0
CD2 A:LEU213 4.3 24.7 1.0
CB A:SER169 4.6 24.8 1.0
CA A:LEU216 4.6 22.8 1.0
C28 A:Y1B907 4.7 26.5 0.7
C A:LEU216 4.7 24.4 1.0
C28 A:Y1B907 4.7 30.6 0.3
N A:ALA217 4.7 21.8 1.0
CG1 A:VAL356 4.8 23.7 1.0
CD2 A:LEU216 4.9 23.8 1.0
OG A:SER169 5.0 28.3 1.0
CA A:LEU213 5.0 24.2 1.0
C19 A:Y1B907 5.0 26.1 0.7
C19 A:Y1B907 5.0 30.0 0.3

Fluorine binding site 7 out of 7 in 7g7z

Go back to Fluorine Binding Sites List in 7g7z
Fluorine binding site 7 out of 7 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]Sulfanylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 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]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F907

b:31.6
occ:0.30
 F26 A:Y1B907 0.0 31.6 0.3
F26 A:Y1B907 0.0 28.1 0.7
C23 A:Y1B907 1.3 28.6 0.7
C23 A:Y1B907 1.3 31.6 0.3
F24 A:Y1B907 2.0 32.1 0.3
F24 A:Y1B907 2.0 29.3 0.7
F25 A:Y1B907 2.1 31.0 0.3
F25 A:Y1B907 2.1 27.1 0.7
C22 A:Y1B907 2.4 26.2 0.7
C22 A:Y1B907 2.4 30.4 0.3
C21 A:Y1B907 2.9 25.8 0.7
C21 A:Y1B907 2.9 29.9 0.3
CB A:LEU216 3.4 21.6 1.0
C27 A:Y1B907 3.5 25.5 0.7
C27 A:Y1B907 3.5 30.0 0.3
CD1 A:LEU216 3.6 26.0 1.0
CG A:LEU216 4.1 23.2 1.0
CG2 A:ILE167 4.1 23.2 1.0
C20 A:Y1B907 4.2 26.2 0.7
C20 A:Y1B907 4.3 30.1 0.3
O A:LEU213 4.3 21.1 1.0
CD2 A:LEU213 4.3 24.7 1.0
CB A:SER169 4.5 24.8 1.0
C28 A:Y1B907 4.7 26.5 0.7
CA A:LEU216 4.7 22.8 1.0
C28 A:Y1B907 4.7 30.6 0.3
C A:LEU216 4.7 24.4 1.0
N A:ALA217 4.7 21.8 1.0
CG1 A:VAL356 4.7 23.7 1.0
CD2 A:LEU216 4.9 23.8 1.0
OG A:SER169 4.9 28.3 1.0
C19 A:Y1B907 5.0 26.1 0.7
CA A:LEU213 5.0 24.2 1.0
C19 A:Y1B907 5.0 30.0 0.3

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 18:07:36 2025

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