Atomistry » Fluorine » PDB 7g2p-7g64 » 7g5p
Atomistry »
  Fluorine »
    PDB 7g2p-7g64 »
      7g5p »

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: Sat Feb 8 17:58:11 2025

Last articles

Au in 5JVX
Au in 5Y0Y
Au in 5Z91
Au in 5Z8S
Au in 5Z8J
Au in 5JJO
Au in 5W1L
Au in 5MVB
Au in 5LYS
Au in 5IX6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy