Atomistry » Fluorine » PDB 7fw1-7g2n » 7g2m
Atomistry »
  Fluorine »
    PDB 7fw1-7g2n »
      7g2m »

Fluorine in PDB 7g2m: Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm, PDB code: 7g2m 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) 48.53 / 2.41
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.891, 91.227, 119.009, 90, 90, 90
R / Rfree (%) 18.9 / 24.5

Other elements in 7g2m:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm (pdb code 7g2m). 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm, PDB code: 7g2m:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 7g2m

Go back to Fluorine Binding Sites List in 7g2m
Fluorine binding site 1 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:74.4
occ:1.00
 F17 A:YQ5901 0.0 74.4 1.0
C16 A:YQ5901 1.3 80.0 1.0
C15 A:YQ5901 2.4 80.0 1.0
C11 A:YQ5901 2.4 80.0 1.0
OH A:TYR306 2.7 50.0 1.0
C9 A:YQ5901 3.0 80.0 1.0
OD2 A:ASP171 3.2 52.7 1.0
N7 A:YQ5901 3.4 71.6 1.0
N12 A:YQ5901 3.6 80.0 1.0
C14 A:YQ5901 3.7 80.0 1.0
CZ A:TYR306 3.8 43.0 1.0
O10 A:YQ5901 3.8 80.0 1.0
C8 A:YQ5901 3.9 67.5 1.0
CE2 A:TYR306 3.9 42.6 1.0
C13 A:YQ5901 4.1 80.0 1.0
CG A:GLU308 4.1 53.6 1.0
CB A:GLU308 4.2 47.5 1.0
C6 A:YQ5901 4.2 64.7 1.0
CA A:GLU308 4.2 43.4 1.0
CG A:ASP171 4.3 44.4 1.0
O A:GLU308 4.7 40.8 1.0
C1 A:YQ5901 4.7 64.9 1.0
C5 A:YQ5901 4.8 65.7 1.0
OD2 A:ASP311 4.9 42.8 1.0
CB A:ASP171 4.9 42.1 1.0
N19 A:YQ5901 5.0 80.0 1.0

Fluorine binding site 2 out of 4 in 7g2m

Go back to Fluorine Binding Sites List in 7g2m
Fluorine binding site 2 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:51.3
occ:1.00
 F40 A:YQ5901 0.0 51.3 1.0
C39 A:YQ5901 1.3 48.3 1.0
F41 A:YQ5901 2.0 51.7 1.0
F42 A:YQ5901 2.2 47.3 1.0
C29 A:YQ5901 2.4 45.1 1.0
C28 A:YQ5901 2.8 44.4 1.0
C30 A:YQ5901 3.5 44.2 1.0
CB A:LEU216 3.6 31.4 1.0
CD1 A:LEU216 3.8 34.5 1.0
CG2 A:ILE167 3.9 35.1 1.0
C27 A:YQ5901 4.2 45.7 1.0
CG A:LEU216 4.3 33.5 1.0
CB A:SER169 4.4 36.8 1.0
O A:LEU213 4.5 36.3 1.0
CG1 A:VAL356 4.6 34.4 1.0
CD2 A:LEU213 4.6 37.7 1.0
C31 A:YQ5901 4.7 47.2 1.0
C A:LEU216 4.8 33.1 1.0
CA A:LEU216 4.9 31.3 1.0
N A:ALA217 4.9 32.5 1.0
OG A:SER169 4.9 40.7 1.0
CD2 A:LEU216 4.9 34.6 1.0
C26 A:YQ5901 4.9 47.1 1.0

Fluorine binding site 3 out of 4 in 7g2m

Go back to Fluorine Binding Sites List in 7g2m
Fluorine binding site 3 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:51.7
occ:1.00
 F41 A:YQ5901 0.0 51.7 1.0
C39 A:YQ5901 1.3 48.3 1.0
F40 A:YQ5901 2.0 51.3 1.0
F42 A:YQ5901 2.1 47.3 1.0
C29 A:YQ5901 2.4 45.1 1.0
C28 A:YQ5901 3.1 44.4 1.0
C30 A:YQ5901 3.3 44.2 1.0
CG2 A:ILE167 3.7 35.1 1.0
CE2 A:PHE273 3.7 47.7 1.0
CD2 A:PHE273 4.0 48.6 1.0
CD1 A:ILE167 4.1 35.6 1.0
C27 A:YQ5901 4.4 45.7 1.0
CB A:ILE167 4.5 33.3 1.0
C31 A:YQ5901 4.5 47.2 1.0
CB A:LEU216 4.7 31.4 1.0
CG1 A:ILE167 4.7 33.8 1.0
CA A:ALA217 4.7 32.8 1.0
CE A:MET512 4.7 40.0 1.0
N A:ALA217 4.7 32.5 1.0
SD A:MET512 4.8 39.2 1.0
C A:LEU216 4.8 33.1 1.0
O A:LEU216 4.9 34.4 1.0
C26 A:YQ5901 4.9 47.1 1.0
CZ A:PHE273 5.0 46.7 1.0

Fluorine binding site 4 out of 4 in 7g2m

Go back to Fluorine Binding Sites List in 7g2m
Fluorine binding site 4 out of 4 in the Crystal Structure of Rat Autotaxin in Complex with 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 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 5-Fluoro-6-[2-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]-1,3,4,6-Tetrahydropyrrolo[3,4-C]Pyrrole-5- Carbonyl]Pyridine-3-Sulfonamide, I.E. Smiles C12=C(Cn(C1)C(=O) CCC1CCC(CC1CN1N=Nc(=N1)C)C(F)(F)F)Cn(C2)C(=O)C1NCC(CC1F)S(=O)(=O)N with IC50=0.0018642 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:47.3
occ:1.00
 F42 A:YQ5901 0.0 47.3 1.0
C39 A:YQ5901 1.3 48.3 1.0
F41 A:YQ5901 2.1 51.7 1.0
F40 A:YQ5901 2.2 51.3 1.0
C29 A:YQ5901 2.4 45.1 1.0
C30 A:YQ5901 2.7 44.2 1.0
O A:LEU213 3.1 36.3 1.0
N A:ALA217 3.1 32.5 1.0
CB A:LEU216 3.4 31.4 1.0
CA A:ALA217 3.4 32.8 1.0
C A:LEU216 3.5 33.1 1.0
CB A:ALA217 3.5 34.9 1.0
C28 A:YQ5901 3.6 44.4 1.0
CA A:LEU216 4.1 31.3 1.0
C31 A:YQ5901 4.1 47.2 1.0
O A:LEU216 4.1 34.4 1.0
C A:LEU213 4.2 35.3 1.0
CG A:LEU216 4.7 33.5 1.0
CA A:LEU213 4.7 36.5 1.0
CD1 A:LEU216 4.7 34.5 1.0
C27 A:YQ5901 4.8 45.7 1.0
N34 A:YQ5901 4.8 51.2 1.0
N A:LEU216 4.8 31.7 1.0
C A:ALA217 4.9 33.4 1.0
C26 A:YQ5901 4.9 47.1 1.0
C32 A:YQ5901 4.9 45.5 1.0
CD2 A:PHE273 5.0 48.6 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

Last articles

Zn in 8S6Z
Zn in 8S4F
Zn in 8RR4
Zn in 8RR3
Zn in 8RR1
Zn in 8RIP
Zn in 8RL5
Zn in 8RIO
Zn in 8RL9
Zn in 8RLA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy