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Fluorine in PDB 7g4h: Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm, PDB code: 7g4h 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) 48.83 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.02, 91.785, 120.026, 90, 90, 90
R / Rfree (%) 20 / 23.8

Other elements in 7g4h:

The structure of Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm (pdb code 7g4h). 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm, PDB code: 7g4h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7g4h

Go back to Fluorine Binding Sites List in 7g4h
Fluorine binding site 1 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.3
occ:0.50
 F33 A:YNB901 0.0 44.3 0.5
C32 A:YNB901 0.9 42.1 0.5
F34 A:YNB901 1.1 42.4 0.5
C32 A:YNB901 1.3 44.5 0.5
F33 A:YNB901 1.3 41.5 0.5
F35 A:YNB901 1.6 41.7 0.5
F35 A:YNB901 2.1 43.6 0.5
F34 A:YNB901 2.2 44.0 0.5
O31 A:YNB901 2.3 44.0 0.5
O31 A:YNB901 2.3 42.3 0.5
C28 A:YNB901 3.3 42.4 0.5
C28 A:YNB901 3.5 46.4 0.5
CB A:LEU216 3.6 24.1 1.0
C27 A:YNB901 3.6 43.0 0.5
C A:LEU216 3.7 24.7 1.0
O A:LEU216 3.8 25.4 1.0
N A:ALA217 3.8 23.7 1.0
CE A:MET512 3.9 23.8 1.0
CA A:ALA217 3.9 23.7 1.0
C29 A:YNB901 4.1 48.3 0.5
SD A:MET512 4.2 27.9 1.0
CA A:LEU216 4.2 23.5 1.0
CB A:ALA217 4.3 22.8 1.0
CG2 A:ILE167 4.4 27.2 1.0
C29 A:YNB901 4.5 42.1 0.5
C27 A:YNB901 4.6 48.4 0.5
O A:LEU213 4.7 24.6 1.0
CG A:LEU216 4.7 25.4 1.0
CE2 A:PHE273 4.8 34.7 1.0
CD1 A:ILE167 4.8 30.0 1.0
CD1 A:LEU216 4.9 26.5 1.0

Fluorine binding site 2 out of 6 in 7g4h

Go back to Fluorine Binding Sites List in 7g4h
Fluorine binding site 2 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:41.5
occ:0.50
 F33 A:YNB901 0.0 41.5 0.5
C32 A:YNB901 1.3 42.1 0.5
F33 A:YNB901 1.3 44.3 0.5
C32 A:YNB901 1.4 44.5 0.5
O31 A:YNB901 1.5 44.0 0.5
F35 A:YNB901 2.1 43.6 0.5
F35 A:YNB901 2.1 41.7 0.5
F34 A:YNB901 2.2 42.4 0.5
O31 A:YNB901 2.3 42.3 0.5
C27 A:YNB901 2.6 43.0 0.5
F34 A:YNB901 2.7 44.0 0.5
C28 A:YNB901 2.7 46.4 0.5
C28 A:YNB901 2.8 42.4 0.5
CB A:ALA217 3.4 22.8 1.0
CA A:ALA217 3.4 23.7 1.0
C29 A:YNB901 3.5 48.3 0.5
C27 A:YNB901 3.5 48.4 0.5
N A:ALA217 3.6 23.7 1.0
C A:LEU216 3.9 24.7 1.0
C26 A:YNB901 4.0 44.1 0.5
CE2 A:PHE273 4.1 34.7 1.0
O A:LEU213 4.1 24.6 1.0
CB A:LEU216 4.2 24.1 1.0
C29 A:YNB901 4.2 42.1 0.5
CD2 A:PHE273 4.2 33.6 1.0
O A:LEU216 4.3 25.4 1.0
CZ3 A:TRP260 4.6 30.0 1.0
C36 A:YNB901 4.6 43.8 0.5
CA A:LEU216 4.7 23.5 1.0
C30 A:YNB901 4.8 49.8 0.5
CE A:MET512 4.8 23.8 1.0
C26 A:YNB901 4.8 50.1 0.5
C A:ALA217 4.9 23.5 1.0

Fluorine binding site 3 out of 6 in 7g4h

Go back to Fluorine Binding Sites List in 7g4h
Fluorine binding site 3 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:44.0
occ:0.50
 F34 A:YNB901 0.0 44.0 0.5
O31 A:YNB901 1.1 42.3 0.5
C32 A:YNB901 1.3 44.5 0.5
F34 A:YNB901 1.6 42.4 0.5
C32 A:YNB901 1.6 42.1 0.5
F35 A:YNB901 2.2 43.6 0.5
C28 A:YNB901 2.2 42.4 0.5
O31 A:YNB901 2.2 44.0 0.5
F33 A:YNB901 2.2 44.3 0.5
F35 A:YNB901 2.6 41.7 0.5
F33 A:YNB901 2.7 41.5 0.5
C28 A:YNB901 2.9 46.4 0.5
C29 A:YNB901 3.0 42.1 0.5
C29 A:YNB901 3.1 48.3 0.5
C27 A:YNB901 3.1 43.0 0.5
CG2 A:ILE167 3.7 27.2 1.0
CB A:LEU216 3.8 24.1 1.0
CD1 A:LEU216 3.9 26.5 1.0
C27 A:YNB901 4.1 48.4 0.5
C30 A:YNB901 4.3 44.2 0.5
CB A:SER169 4.3 28.7 1.0
C26 A:YNB901 4.3 44.1 0.5
C30 A:YNB901 4.4 49.8 0.5
CG A:LEU216 4.4 25.4 1.0
CG1 A:VAL356 4.5 23.1 1.0
OG A:SER169 4.8 32.9 1.0
CD2 A:LEU213 4.8 23.3 1.0
O A:LEU213 4.8 24.6 1.0
CB A:ILE167 4.8 28.0 1.0
C25 A:YNB901 4.8 46.5 0.5

Fluorine binding site 4 out of 6 in 7g4h

Go back to Fluorine Binding Sites List in 7g4h
Fluorine binding site 4 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:42.4
occ:0.50
 F34 A:YNB901 0.0 42.4 0.5
F33 A:YNB901 1.1 44.3 0.5
C32 A:YNB901 1.3 42.1 0.5
C32 A:YNB901 1.5 44.5 0.5
F34 A:YNB901 1.6 44.0 0.5
F35 A:YNB901 2.1 41.7 0.5
O31 A:YNB901 2.2 42.3 0.5
F33 A:YNB901 2.2 41.5 0.5
F35 A:YNB901 2.5 43.6 0.5
O31 A:YNB901 2.6 44.0 0.5
CB A:LEU216 3.0 24.1 1.0
C28 A:YNB901 3.4 42.4 0.5
C28 A:YNB901 3.8 46.4 0.5
C A:LEU216 3.8 24.7 1.0
C27 A:YNB901 3.9 43.0 0.5
CG A:LEU216 4.0 25.4 1.0
CD1 A:LEU216 4.0 26.5 1.0
CG2 A:ILE167 4.0 27.2 1.0
O A:LEU216 4.0 25.4 1.0
CA A:LEU216 4.1 23.5 1.0
N A:ALA217 4.2 23.7 1.0
CE A:MET512 4.2 23.8 1.0
C29 A:YNB901 4.3 48.3 0.5
CD2 A:LEU216 4.4 26.1 1.0
SD A:MET512 4.4 27.9 1.0
C29 A:YNB901 4.4 42.1 0.5
CA A:ALA217 4.6 23.7 1.0
O A:LEU213 4.8 24.6 1.0
CG1 A:VAL356 4.8 23.1 1.0
C27 A:YNB901 4.9 48.4 0.5

Fluorine binding site 5 out of 6 in 7g4h

Go back to Fluorine Binding Sites List in 7g4h
Fluorine binding site 5 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:43.6
occ:0.50
 F35 A:YNB901 0.0 43.6 0.5
O31 A:YNB901 1.3 42.3 0.5
C32 A:YNB901 1.3 42.1 0.5
C32 A:YNB901 1.3 44.5 0.5
F35 A:YNB901 1.3 41.7 0.5
F33 A:YNB901 2.1 41.5 0.5
C28 A:YNB901 2.1 42.4 0.5
F33 A:YNB901 2.1 44.3 0.5
F34 A:YNB901 2.2 44.0 0.5
O31 A:YNB901 2.3 44.0 0.5
F34 A:YNB901 2.5 42.4 0.5
C29 A:YNB901 2.7 48.3 0.5
C28 A:YNB901 2.8 46.4 0.5
C27 A:YNB901 2.8 43.0 0.5
C29 A:YNB901 3.0 42.1 0.5
CE2 A:PHE273 3.5 34.7 1.0
CG2 A:ILE167 3.5 27.2 1.0
CD2 A:PHE273 3.6 33.6 1.0
CB A:ILE167 3.9 28.0 1.0
C30 A:YNB901 4.0 49.8 0.5
CD1 A:ILE167 4.0 30.0 1.0
C26 A:YNB901 4.1 44.1 0.5
C27 A:YNB901 4.1 48.4 0.5
C30 A:YNB901 4.2 44.2 0.5
CG1 A:ILE167 4.4 27.9 1.0
CB A:ALA304 4.4 29.2 1.0
C25 A:YNB901 4.6 46.5 0.5
CZ A:PHE273 4.7 32.1 1.0
CG A:PHE273 5.0 35.5 1.0

Fluorine binding site 6 out of 6 in 7g4h

Go back to Fluorine Binding Sites List in 7g4h
Fluorine binding site 6 out of 6 in the Crystal Structure of Rat Autotaxin in Complex with [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 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 [2-Methyl-4- (Trifluoromethoxy)Phenyl]Methyl 2-(1,4,6,7-Tetrahydrotriazolo[4,5- C]Pyridine-5-Carbonyl)-6,7-Dihydro-4H-Pyrazolo[1,5-A]Pyrazine-5- Carboxylate, I.E. Smiles N1(CCN2C(=Cc(=N2)C(=O)N2CCC3=C(C2)N=NN3)C1) C(=O)OCC1C(Cc(CC1)Oc(F)(F)F)C with IC50=0.268343 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:41.7
occ:0.50
 F35 A:YNB901 0.0 41.7 0.5
C32 A:YNB901 1.3 42.1 0.5
F35 A:YNB901 1.3 43.6 0.5
F33 A:YNB901 1.6 44.3 0.5
C32 A:YNB901 1.8 44.5 0.5
F33 A:YNB901 2.1 41.5 0.5
F34 A:YNB901 2.1 42.4 0.5
O31 A:YNB901 2.2 42.3 0.5
F34 A:YNB901 2.6 44.0 0.5
O31 A:YNB901 3.0 44.0 0.5
C28 A:YNB901 3.3 42.4 0.5
CD1 A:ILE167 3.3 30.0 1.0
CG2 A:ILE167 3.4 27.2 1.0
CE2 A:PHE273 3.7 34.7 1.0
CG1 A:ILE167 3.7 27.9 1.0
CB A:ILE167 3.8 28.0 1.0
C28 A:YNB901 3.9 46.4 0.5
SD A:MET512 3.9 27.9 1.0
C27 A:YNB901 3.9 43.0 0.5
C29 A:YNB901 4.0 48.3 0.5
CE A:MET512 4.1 23.8 1.0
C29 A:YNB901 4.3 42.1 0.5
CD2 A:PHE273 4.3 33.6 1.0
CD2 A:LEU259 4.7 22.7 1.0
CZ A:PHE273 4.8 32.1 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 17:51:55 2025

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