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Fluorine in PDB 7g7s: Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm, PDB code: 7g7s was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.128, 91.81, 119.923, 90, 90, 90
R / Rfree (%) 19.3 / 22.9

Other elements in 7g7s:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm (pdb code 7g7s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm, PDB code: 7g7s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7g7s

Go back to Fluorine Binding Sites List in 7g7s
Fluorine binding site 1 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:37.7
occ:1.00
 F6 A:Y2L901 0.0 37.7 1.0
C5 A:Y2L901 1.3 37.1 1.0
F8 A:Y2L901 2.1 42.9 1.0
F7 A:Y2L901 2.1 40.3 1.0
C4 A:Y2L901 2.3 35.8 1.0
C9 A:Y2L901 3.0 34.6 1.0
C3 A:Y2L901 3.4 34.8 1.0
CG2 A:ILE167 3.5 26.2 1.0
CD2 A:PHE273 3.5 30.4 1.0
CE2 A:PHE273 3.7 33.3 1.0
CD1 A:ILE167 3.9 31.1 1.0
CB A:ILE167 4.2 27.6 1.0
C10 A:Y2L901 4.2 35.0 1.0
CB A:ALA304 4.4 26.9 1.0
C2 A:Y2L901 4.6 37.1 1.0
CG1 A:ILE167 4.7 27.2 1.0
CG A:PHE273 4.8 33.1 1.0
C11 A:Y2L901 4.9 35.6 1.0
CZ A:PHE273 5.0 33.5 1.0
OG A:SER169 5.0 36.0 1.0
CB A:SER169 5.0 28.7 1.0

Fluorine binding site 2 out of 6 in 7g7s

Go back to Fluorine Binding Sites List in 7g7s
Fluorine binding site 2 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:40.3
occ:1.00
 F7 A:Y2L901 0.0 40.3 1.0
C5 A:Y2L901 1.3 37.1 1.0
F8 A:Y2L901 2.1 42.9 1.0
F6 A:Y2L901 2.1 37.7 1.0
C4 A:Y2L901 2.4 35.8 1.0
C3 A:Y2L901 2.7 34.8 1.0
CB A:ALA217 3.5 23.5 1.0
N A:ALA217 3.5 24.9 1.0
CA A:ALA217 3.6 25.2 1.0
C9 A:Y2L901 3.6 34.6 1.0
O A:LEU213 3.7 24.4 1.0
CB A:LEU216 4.0 24.4 1.0
CD2 A:PHE273 4.0 30.4 1.0
C A:LEU216 4.1 26.3 1.0
C2 A:Y2L901 4.1 37.1 1.0
CE2 A:PHE273 4.3 33.3 1.0
CZ3 A:TRP260 4.6 30.7 1.0
O A:LEU216 4.6 25.4 1.0
CA A:LEU216 4.6 24.4 1.0
C A:LEU213 4.7 24.1 1.0
C10 A:Y2L901 4.8 35.0 1.0
C11 A:Y2L901 4.9 35.6 1.0
C1 A:Y2L901 5.0 38.8 1.0

Fluorine binding site 3 out of 6 in 7g7s

Go back to Fluorine Binding Sites List in 7g7s
Fluorine binding site 3 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:42.9
occ:1.00
 F8 A:Y2L901 0.0 42.9 1.0
C5 A:Y2L901 1.3 37.1 1.0
F6 A:Y2L901 2.1 37.7 1.0
F7 A:Y2L901 2.1 40.3 1.0
C4 A:Y2L901 2.4 35.8 1.0
C9 A:Y2L901 2.9 34.6 1.0
C3 A:Y2L901 3.5 34.8 1.0
CB A:LEU216 3.5 24.4 1.0
CD1 A:LEU216 3.6 28.9 1.0
CG A:LEU216 4.2 28.5 1.0
C10 A:Y2L901 4.2 35.0 1.0
O A:LEU213 4.2 24.4 1.0
CD2 A:LEU213 4.3 26.6 1.0
CG2 A:ILE167 4.4 26.2 1.0
CB A:SER169 4.5 28.7 1.0
C2 A:Y2L901 4.6 37.1 1.0
N A:ALA217 4.8 24.9 1.0
CA A:LEU213 4.8 25.3 1.0
CA A:LEU216 4.8 24.4 1.0
OG A:SER169 4.8 36.0 1.0
C A:LEU216 4.8 26.3 1.0
C11 A:Y2L901 4.9 35.6 1.0
CB A:LEU213 4.9 25.0 1.0
C A:LEU213 5.0 24.1 1.0

Fluorine binding site 4 out of 6 in 7g7s

Go back to Fluorine Binding Sites List in 7g7s
Fluorine binding site 4 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:80.0
occ:1.00
 F6 A:Y2L902 0.0 80.0 1.0
C5 A:Y2L902 1.3 74.7 1.0
F7 A:Y2L902 2.1 79.1 1.0
F8 A:Y2L902 2.1 73.9 1.0
C4 A:Y2L902 2.4 67.9 1.0
C3 A:Y2L902 3.2 64.8 1.0
CE2 A:PHE274 3.2 48.7 1.0
C9 A:Y2L902 3.3 60.6 1.0
CD2 A:PHE274 3.5 46.2 1.0
CE2 A:PHE210 3.7 43.9 1.0
CZ A:PHE210 3.9 40.8 1.0
CH2 A:TRP254 4.1 40.4 1.0
CZ2 A:TRP254 4.3 39.2 1.0
CZ A:PHE274 4.3 45.2 1.0
O19 A:Y2L901 4.3 56.2 1.0
C2 A:Y2L902 4.4 64.8 1.0
C10 A:Y2L902 4.5 63.5 1.0
CD2 A:PHE210 4.6 40.5 1.0
N22 A:Y2L901 4.7 47.1 1.0
C16 A:Y2L901 4.7 49.4 1.0
CG A:PHE274 4.7 46.0 1.0
C20 A:Y2L901 4.8 42.2 1.0
C26 A:Y2L901 4.8 45.3 1.0
CE A:LYS248 4.8 64.4 1.0
C23 A:Y2L901 4.9 46.9 1.0
N15 A:Y2L901 4.9 46.9 1.0
C11 A:Y2L902 5.0 63.7 1.0

Fluorine binding site 5 out of 6 in 7g7s

Go back to Fluorine Binding Sites List in 7g7s
Fluorine binding site 5 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm


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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:79.1
occ:1.00
 F7 A:Y2L902 0.0 79.1 1.0
C5 A:Y2L902 1.4 74.7 1.0
F6 A:Y2L902 2.1 80.0 1.0
F8 A:Y2L902 2.2 73.9 1.0
C4 A:Y2L902 2.4 67.9 1.0
C3 A:Y2L902 2.8 64.8 1.0
CE A:LYS248 3.0 64.4 1.0
CD A:LYS248 3.2 62.4 1.0
C9 A:Y2L902 3.6 60.6 1.0
CG A:LYS248 3.6 62.7 1.0
CE2 A:PHE210 3.7 43.9 1.0
CB A:LYS248 4.1 57.8 1.0
CZ2 A:TRP254 4.2 39.2 1.0
CZ A:PHE210 4.2 40.8 1.0
C2 A:Y2L902 4.2 64.8 1.0
O A:LYS248 4.3 61.9 1.0
CE1 A:PHE249 4.5 72.0 1.0
NZ A:LYS248 4.5 59.7 1.0
CH2 A:TRP254 4.5 40.4 1.0
C A:LYS248 4.6 59.3 1.0
CD1 A:PHE249 4.7 70.3 1.0
CZ A:PHE249 4.8 68.8 1.0
C10 A:Y2L902 4.8 63.5 1.0
CD2 A:PHE210 4.8 40.5 1.0

Fluorine binding site 6 out of 6 in 7g7s

Go back to Fluorine Binding Sites List in 7g7s
Fluorine binding site 6 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm


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 4-Methyl-3-[[2-[(5- Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl)Phenoxy]Methyl]-1H-1, 2,4-Triazol-5-One, I.E. Smiles C(C1CC(C(F)(F)F)CCC1OCC1=Nnc(=O)N1C) N1N=C(N=N1)C with IC50=2.52664 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F902

b:73.9
occ:1.00
 F8 A:Y2L902 0.0 73.9 1.0
C5 A:Y2L902 1.4 74.7 1.0
F6 A:Y2L902 2.1 80.0 1.0
F7 A:Y2L902 2.2 79.1 1.0
C4 A:Y2L902 2.4 67.9 1.0
C9 A:Y2L902 2.8 60.6 1.0
CE A:LYS248 3.7 64.4 1.0
C3 A:Y2L902 3.7 64.8 1.0
O19 A:Y2L901 3.9 56.2 1.0
CE1 A:PHE249 4.1 72.0 1.0
C10 A:Y2L902 4.2 63.5 1.0
CD2 A:PHE274 4.3 46.2 1.0
CZ A:PHE249 4.4 68.8 1.0
C16 A:Y2L901 4.5 49.4 1.0
CD A:LYS248 4.6 62.4 1.0
CE2 A:PHE274 4.6 48.7 1.0
CZ A:PHE210 4.7 40.8 1.0
NZ A:LYS248 4.7 59.7 1.0
CE2 A:PHE210 4.7 43.9 1.0
CD1 A:PHE249 4.8 70.3 1.0
C2 A:Y2L902 4.9 64.8 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 18:05:15 2025

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