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Fluorine in PDB 7g5p: Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm, PDB code: 7g5p was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.203, 92.065, 119.91, 90, 90, 90
R / Rfree (%) 18.5 / 21.5

Other elements in 7g5p:

The structure of Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Sodium (Na) 2 atoms
Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm (pdb code 7g5p). 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 N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm, PDB code: 7g5p:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7g5p

Go back to Fluorine Binding Sites List in 7g5p
Fluorine binding site 1 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 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 N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:22.2
occ:1.00
 F37 A:Y8Z901 0.0 22.2 1.0
C36 A:Y8Z901 1.3 21.3 1.0
F38 A:Y8Z901 2.1 21.5 1.0
F39 A:Y8Z901 2.1 19.6 1.0
C32 A:Y8Z901 2.4 19.4 1.0
C31 A:Y8Z901 3.1 20.8 1.0
CL40 A:Y8Z901 3.3 45.7 1.0
C34 A:Y8Z901 3.4 17.6 1.0
CB A:LEU216 3.6 12.9 1.0
CD1 A:LEU216 3.8 15.4 1.0
CG2 A:ILE167 4.0 14.6 1.0
CG A:LEU216 4.3 13.6 1.0
C33 A:Y8Z901 4.4 20.7 1.0
O A:LEU213 4.5 10.8 1.0
CB A:SER169 4.5 19.7 1.0
CD2 A:LEU213 4.5 16.2 1.0
C29 A:Y8Z901 4.6 16.8 1.0
CG1 A:VAL356 4.7 14.1 1.0
OG A:SER169 4.7 24.5 1.0
CA A:LEU216 4.8 12.5 1.0
C A:LEU216 4.9 12.1 1.0
CD2 A:LEU216 4.9 14.2 1.0
N A:ALA217 4.9 11.4 1.0

Fluorine binding site 2 out of 3 in 7g5p

Go back to Fluorine Binding Sites List in 7g5p
Fluorine binding site 2 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 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 N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:21.5
occ:1.00
 F38 A:Y8Z901 0.0 21.5 1.0
C36 A:Y8Z901 1.4 21.3 1.0
F39 A:Y8Z901 2.1 19.6 1.0
F37 A:Y8Z901 2.1 22.2 1.0
C32 A:Y8Z901 2.4 19.4 1.0
CL40 A:Y8Z901 2.9 45.7 1.0
C31 A:Y8Z901 2.9 20.8 1.0
C34 A:Y8Z901 3.6 17.6 1.0
CG2 A:ILE167 3.6 14.6 1.0
CD1 A:ILE167 3.6 16.6 1.0
CE2 A:PHE273 3.6 19.4 1.0
CD2 A:PHE273 4.0 18.5 1.0
CB A:ILE167 4.1 15.2 1.0
C33 A:Y8Z901 4.3 20.7 1.0
CG1 A:ILE167 4.3 15.2 1.0
C29 A:Y8Z901 4.7 16.8 1.0
CZ A:PHE273 4.8 19.9 1.0
CB A:ALA304 4.9 17.3 1.0
CE A:MET512 4.9 14.3 1.0
SD A:MET512 5.0 17.2 1.0
CB A:LEU216 5.0 12.9 1.0

Fluorine binding site 3 out of 3 in 7g5p

Go back to Fluorine Binding Sites List in 7g5p
Fluorine binding site 3 out of 3 in the Crystal Structure of Rat Autotaxin in Complex with N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 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 N-[(1R,3S)-3-[(2S)- 2-Benzyl-4-[2-(Methylamino)-2-Oxoethyl]-3-Oxopiperazine-1- Carbonyl]Cyclopentyl]-4-Chloro-3-(Trifluoromethyl)Benzamide, I.E. Smiles C1[C@@H](Cc[C@@H]1C(=O)N1CCN(C(=O)[C@@H]1CC1CCCCC1)Cc(=O)Nc) Nc(=O)C1CCC(C(C1)C(F)(F)F)Cl with IC50=0.17269 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:19.6
occ:1.00
 F39 A:Y8Z901 0.0 19.6 1.0
C36 A:Y8Z901 1.3 21.3 1.0
F38 A:Y8Z901 2.1 21.5 1.0
F37 A:Y8Z901 2.1 22.2 1.0
C32 A:Y8Z901 2.4 19.4 1.0
C34 A:Y8Z901 2.8 17.6 1.0
N A:ALA217 3.2 11.4 1.0
CA A:ALA217 3.4 11.7 1.0
CB A:LEU216 3.4 12.9 1.0
C A:LEU216 3.5 12.1 1.0
CB A:ALA217 3.6 12.4 1.0
O A:LEU213 3.6 10.8 1.0
C31 A:Y8Z901 3.7 20.8 1.0
O A:LEU216 4.0 12.3 1.0
CA A:LEU216 4.0 12.5 1.0
C29 A:Y8Z901 4.2 16.8 1.0
CL40 A:Y8Z901 4.4 45.7 1.0
CE A:MET512 4.7 14.3 1.0
CG A:LEU216 4.7 13.6 1.0
C A:LEU213 4.7 11.6 1.0
CE2 A:PHE273 4.8 19.4 1.0
CD1 A:LEU216 4.8 15.4 1.0
C A:ALA217 4.8 12.7 1.0
C33 A:Y8Z901 4.8 20.7 1.0
O35 A:Y8Z901 4.9 14.7 1.0
N A:LEU216 4.9 10.3 1.0
CD2 A:PHE273 5.0 18.5 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: Tue Jul 15 20:01:15 2025

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