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Fluorine in PDB 3ln0: Structure of Compound 5C-S Bound at the Active Site of Cox-2

Enzymatic activity of Structure of Compound 5C-S Bound at the Active Site of Cox-2

All present enzymatic activity of Structure of Compound 5C-S Bound at the Active Site of Cox-2:
1.14.99.1;

Protein crystallography data

The structure of Structure of Compound 5C-S Bound at the Active Site of Cox-2, PDB code: 3ln0 was solved by J.R.Kiefer, R.G.Kurumbail, W.C.Stallings, J.L.Pawlitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.96 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 181.015, 135.201, 124.291, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 23.8

Other elements in 3ln0:

The structure of Structure of Compound 5C-S Bound at the Active Site of Cox-2 also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 8 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Structure of Compound 5C-S Bound at the Active Site of Cox-2 (pdb code 3ln0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Structure of Compound 5C-S Bound at the Active Site of Cox-2, PDB code: 3ln0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 1 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:27.0
occ:1.00
 F1 A:52B701 0.0 27.0 1.0
C14 A:52B701 1.4 26.4 1.0
F2 A:52B701 2.2 25.8 1.0
F3 A:52B701 2.2 28.5 1.0
C9 A:52B701 2.4 26.9 1.0
O11 A:52B701 2.9 26.0 1.0
CE2 A:PHE504 3.5 25.6 1.0
CD2 A:PHE504 3.7 26.1 1.0
C8 A:52B701 3.7 27.1 1.0
C6 A:52B701 3.9 27.9 1.0
O A:MET508 3.9 25.4 1.0
CA A:VAL509 3.9 25.5 1.0
CG A:MET508 4.1 24.9 1.0
C A:MET508 4.2 25.5 1.0
O12 A:52B701 4.3 26.4 1.0
CZ2 A:TRP373 4.3 20.9 1.0
CG2 A:VAL509 4.3 25.3 1.0
N A:VAL509 4.3 25.4 1.0
CH2 A:TRP373 4.4 20.6 1.0
CZ A:PHE504 4.5 24.4 1.0
C10 A:52B701 4.5 26.4 1.0
CL2 A:52B701 4.5 34.4 1.0
C2 A:52B701 4.5 28.8 1.0
C7 A:52B701 4.6 25.7 1.0
CB A:VAL509 4.6 25.6 1.0
C3 A:52B701 4.6 27.5 1.0
CG A:PHE504 4.7 26.1 1.0
CA A:GLY512 4.8 24.7 1.0
O A:VAL509 4.9 25.8 1.0
C A:VAL509 4.9 25.8 1.0
CB A:MET508 4.9 25.4 1.0
CG1 A:VAL509 5.0 25.2 1.0

Fluorine binding site 2 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 2 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:25.8
occ:1.00
 F2 A:52B701 0.0 25.8 1.0
C14 A:52B701 1.4 26.4 1.0
F1 A:52B701 2.2 27.0 1.0
F3 A:52B701 2.2 28.5 1.0
C9 A:52B701 2.4 26.9 1.0
O11 A:52B701 2.8 26.0 1.0
C8 A:52B701 3.0 27.1 1.0
N A:ALA513 3.0 24.1 1.0
C6 A:52B701 3.0 27.9 1.0
C A:GLY512 3.2 24.5 1.0
C3 A:52B701 3.3 27.5 1.0
C7 A:52B701 3.4 25.7 1.0
CA A:GLY512 3.5 24.7 1.0
O A:VAL509 3.5 25.8 1.0
CA A:ALA513 3.6 24.2 1.0
CA A:VAL509 3.7 25.5 1.0
C2 A:52B701 3.8 28.8 1.0
O A:MET508 3.9 25.4 1.0
O A:GLY512 3.9 24.5 1.0
CB A:ALA513 4.0 23.8 1.0
C A:VAL509 4.1 25.8 1.0
C10 A:52B701 4.1 26.4 1.0
N A:GLY512 4.2 24.7 1.0
C1 A:52B701 4.2 27.9 1.0
CG1 A:VAL509 4.4 25.2 1.0
O12 A:52B701 4.4 26.4 1.0
CL2 A:52B701 4.5 34.4 1.0
CB A:VAL509 4.5 25.6 1.0
C A:MET508 4.6 25.5 1.0
N A:VAL509 4.6 25.4 1.0
C5 A:52B701 4.6 28.9 1.0
C4 A:52B701 4.8 29.4 1.0
CG2 A:VAL509 4.9 25.3 1.0
O13 A:52B701 5.0 25.2 1.0
C A:ALA513 5.0 24.3 1.0

Fluorine binding site 3 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 3 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:28.5
occ:1.00
 F3 A:52B701 0.0 28.5 1.0
C14 A:52B701 1.4 26.4 1.0
F1 A:52B701 2.2 27.0 1.0
F2 A:52B701 2.2 25.8 1.0
C9 A:52B701 2.4 26.9 1.0
C8 A:52B701 2.8 27.1 1.0
O12 A:52B701 2.8 26.4 1.0
C10 A:52B701 3.0 26.4 1.0
O11 A:52B701 3.6 26.0 1.0
CA A:GLY512 3.7 24.7 1.0
C7 A:52B701 3.8 25.7 1.0
C A:GLY512 3.9 24.5 1.0
CZ2 A:TRP373 3.9 20.9 1.0
CH2 A:TRP373 4.0 20.6 1.0
O13 A:52B701 4.1 25.2 1.0
O A:GLY512 4.1 24.5 1.0
CE1 A:TYR371 4.3 19.6 1.0
C6 A:52B701 4.3 27.9 1.0
O A:MET508 4.4 25.4 1.0
N A:ALA513 4.4 24.1 1.0
C3 A:52B701 4.4 27.5 1.0
CD1 A:LEU370 4.7 23.6 1.0
N A:GLY512 4.8 24.7 1.0
OH A:TYR371 4.8 18.9 1.0
CZ A:TYR371 4.9 20.0 1.0
CE1 A:PHE367 4.9 23.6 1.0
CD1 A:TYR371 4.9 20.5 1.0

Fluorine binding site 4 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 4 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:27.5
occ:1.00
 F1 B:52B701 0.0 27.5 1.0
C14 B:52B701 1.4 27.7 1.0
F3 B:52B701 2.2 27.6 1.0
F2 B:52B701 2.2 28.0 1.0
C9 B:52B701 2.4 27.1 1.0
O11 B:52B701 2.9 28.1 1.0
CE2 B:PHE504 3.5 25.4 1.0
CD2 B:PHE504 3.7 26.1 1.0
C8 B:52B701 3.7 26.3 1.0
O B:MET508 3.8 25.3 1.0
C6 B:52B701 3.9 28.2 1.0
CA B:VAL509 4.0 25.5 1.0
CG B:MET508 4.1 24.9 1.0
O12 B:52B701 4.2 24.8 1.0
CZ2 B:TRP373 4.2 20.5 1.0
C B:MET508 4.3 25.4 1.0
CG2 B:VAL509 4.3 25.2 1.0
N B:VAL509 4.4 25.4 1.0
CH2 B:TRP373 4.4 20.7 1.0
CZ B:PHE504 4.4 24.4 1.0
C10 B:52B701 4.5 25.9 1.0
CL2 B:52B701 4.5 32.1 1.0
C2 B:52B701 4.6 29.8 1.0
C7 B:52B701 4.6 26.2 1.0
C3 B:52B701 4.7 28.1 1.0
CB B:VAL509 4.7 25.8 1.0
CG B:PHE504 4.7 26.3 1.0
CA B:GLY512 4.7 24.6 1.0
O B:VAL509 4.9 25.9 1.0
CB B:MET508 4.9 25.3 1.0
C B:VAL509 5.0 25.8 1.0

Fluorine binding site 5 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 5 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:28.0
occ:1.00
 F2 B:52B701 0.0 28.0 1.0
C14 B:52B701 1.4 27.7 1.0
F3 B:52B701 2.2 27.6 1.0
F1 B:52B701 2.2 27.5 1.0
C9 B:52B701 2.5 27.1 1.0
O11 B:52B701 2.9 28.1 1.0
N B:ALA513 3.0 24.3 1.0
C6 B:52B701 3.0 28.2 1.0
C8 B:52B701 3.1 26.3 1.0
C B:GLY512 3.3 24.7 1.0
C3 B:52B701 3.3 28.1 1.0
O B:VAL509 3.5 25.9 1.0
C7 B:52B701 3.5 26.2 1.0
CA B:GLY512 3.5 24.6 1.0
CA B:ALA513 3.5 24.2 1.0
CA B:VAL509 3.7 25.5 1.0
C2 B:52B701 3.8 29.8 1.0
O B:MET508 3.9 25.3 1.0
CB B:ALA513 3.9 23.9 1.0
C B:VAL509 4.0 25.8 1.0
O B:GLY512 4.0 24.9 1.0
C10 B:52B701 4.2 25.9 1.0
C1 B:52B701 4.2 28.1 1.0
N B:GLY512 4.2 24.8 1.0
CG1 B:VAL509 4.4 25.1 1.0
CL2 B:52B701 4.4 32.1 1.0
CB B:VAL509 4.5 25.8 1.0
O12 B:52B701 4.5 24.8 1.0
N B:VAL509 4.6 25.4 1.0
C B:MET508 4.6 25.4 1.0
C5 B:52B701 4.6 29.6 1.0
C4 B:52B701 4.8 29.6 1.0
CG2 B:VAL509 4.8 25.2 1.0
C B:ALA513 5.0 24.3 1.0

Fluorine binding site 6 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 6 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F701

b:27.6
occ:1.00
 F3 B:52B701 0.0 27.6 1.0
C14 B:52B701 1.4 27.7 1.0
F2 B:52B701 2.2 28.0 1.0
F1 B:52B701 2.2 27.5 1.0
C9 B:52B701 2.4 27.1 1.0
C8 B:52B701 2.8 26.3 1.0
O12 B:52B701 3.0 24.8 1.0
C10 B:52B701 3.1 25.9 1.0
CA B:GLY512 3.5 24.6 1.0
O11 B:52B701 3.7 28.1 1.0
C B:GLY512 3.7 24.7 1.0
C7 B:52B701 3.8 26.2 1.0
O B:GLY512 4.0 24.9 1.0
O13 B:52B701 4.1 27.3 1.0
CZ2 B:TRP373 4.1 20.5 1.0
N B:ALA513 4.1 24.3 1.0
CH2 B:TRP373 4.2 20.7 1.0
O B:MET508 4.3 25.3 1.0
C6 B:52B701 4.3 28.2 1.0
CE1 B:TYR371 4.4 19.5 1.0
C3 B:52B701 4.4 28.1 1.0
N B:GLY512 4.7 24.8 1.0
CD1 B:LEU370 4.7 23.4 1.0
CE1 B:PHE367 4.8 23.5 1.0
CA B:ALA513 4.9 24.2 1.0

Fluorine binding site 7 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 7 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:26.7
occ:1.00
 F1 C:52B701 0.0 26.7 1.0
C14 C:52B701 1.4 25.7 1.0
F3 C:52B701 2.2 25.9 1.0
F2 C:52B701 2.2 25.1 1.0
C9 C:52B701 2.4 24.9 1.0
O11 C:52B701 2.9 25.7 1.0
CE2 C:PHE504 3.5 25.5 1.0
C8 C:52B701 3.7 24.7 1.0
CD2 C:PHE504 3.7 26.1 1.0
O C:MET508 3.8 25.2 1.0
C6 C:52B701 3.9 26.1 1.0
CA C:VAL509 4.0 25.4 1.0
CG C:MET508 4.0 24.9 1.0
CZ2 C:TRP373 4.2 20.7 1.0
C C:MET508 4.2 25.4 1.0
O12 C:52B701 4.3 25.1 1.0
N C:VAL509 4.3 25.3 1.0
CG2 C:VAL509 4.4 25.1 1.0
CH2 C:TRP373 4.4 20.6 1.0
CZ C:PHE504 4.4 24.4 1.0
C10 C:52B701 4.5 24.9 1.0
CL2 C:52B701 4.5 31.4 1.0
C7 C:52B701 4.6 24.9 1.0
C2 C:52B701 4.6 27.6 1.0
C3 C:52B701 4.6 25.8 1.0
CB C:VAL509 4.7 25.7 1.0
CA C:GLY512 4.7 24.6 1.0
CG C:PHE504 4.7 26.1 1.0
CB C:MET508 4.9 25.3 1.0
O C:VAL509 4.9 25.7 1.0
C C:VAL509 5.0 25.8 1.0

Fluorine binding site 8 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 8 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:25.1
occ:1.00
 F2 C:52B701 0.0 25.1 1.0
C14 C:52B701 1.4 25.7 1.0
F3 C:52B701 2.2 25.9 1.0
F1 C:52B701 2.2 26.7 1.0
C9 C:52B701 2.4 24.9 1.0
O11 C:52B701 2.9 25.7 1.0
N C:ALA513 3.0 24.4 1.0
C6 C:52B701 3.0 26.1 1.0
C8 C:52B701 3.1 24.7 1.0
C C:GLY512 3.2 24.6 1.0
C3 C:52B701 3.3 25.8 1.0
C7 C:52B701 3.4 24.9 1.0
O C:VAL509 3.4 25.7 1.0
CA C:GLY512 3.5 24.6 1.0
CA C:ALA513 3.5 24.1 1.0
CA C:VAL509 3.7 25.4 1.0
C2 C:52B701 3.8 27.6 1.0
O C:MET508 3.8 25.2 1.0
CB C:ALA513 3.9 23.8 1.0
O C:GLY512 4.0 24.6 1.0
C C:VAL509 4.0 25.8 1.0
N C:GLY512 4.2 24.7 1.0
C10 C:52B701 4.2 24.9 1.0
C1 C:52B701 4.2 26.7 1.0
CG1 C:VAL509 4.4 25.2 1.0
CL2 C:52B701 4.4 31.4 1.0
CB C:VAL509 4.5 25.7 1.0
O12 C:52B701 4.5 25.1 1.0
N C:VAL509 4.6 25.3 1.0
C C:MET508 4.6 25.4 1.0
C5 C:52B701 4.6 27.6 1.0
C4 C:52B701 4.8 28.1 1.0
CG2 C:VAL509 4.9 25.1 1.0
C C:ALA513 5.0 24.2 1.0

Fluorine binding site 9 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 9 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F701

b:25.9
occ:1.00
 F3 C:52B701 0.0 25.9 1.0
C14 C:52B701 1.4 25.7 1.0
F1 C:52B701 2.2 26.7 1.0
F2 C:52B701 2.2 25.1 1.0
C9 C:52B701 2.4 24.9 1.0
C8 C:52B701 2.8 24.7 1.0
O12 C:52B701 3.0 25.1 1.0
C10 C:52B701 3.1 24.9 1.0
CA C:GLY512 3.5 24.6 1.0
O11 C:52B701 3.6 25.7 1.0
C C:GLY512 3.7 24.6 1.0
C7 C:52B701 3.8 24.9 1.0
O C:GLY512 4.0 24.6 1.0
CZ2 C:TRP373 4.1 20.7 1.0
O13 C:52B701 4.1 24.8 1.0
N C:ALA513 4.2 24.4 1.0
CH2 C:TRP373 4.2 20.6 1.0
O C:MET508 4.2 25.2 1.0
C6 C:52B701 4.3 26.1 1.0
CE1 C:TYR371 4.4 19.5 1.0
C3 C:52B701 4.4 25.8 1.0
CD1 C:LEU370 4.6 23.4 1.0
N C:GLY512 4.6 24.7 1.0
CE1 C:PHE367 4.8 23.6 1.0
CA C:ALA513 4.9 24.1 1.0
CD1 C:TYR371 5.0 20.6 1.0

Fluorine binding site 10 out of 12 in 3ln0

Go back to Fluorine Binding Sites List in 3ln0
Fluorine binding site 10 out of 12 in the Structure of Compound 5C-S Bound at the Active Site of Cox-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of Compound 5C-S Bound at the Active Site of Cox-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F701

b:26.9
occ:1.00
 F1 D:52B701 0.0 26.9 1.0
C14 D:52B701 1.3 25.4 1.0
F2 D:52B701 2.1 22.9 1.0
F3 D:52B701 2.1 25.2 1.0
C9 D:52B701 2.4 26.3 1.0
O11 D:52B701 2.9 27.4 1.0
CE2 D:PHE504 3.7 25.7 1.0
CA D:VAL509 3.7 25.4 1.0
C8 D:52B701 3.7 26.3 1.0
CD2 D:PHE504 3.8 26.1 1.0
O D:MET508 3.8 25.1 1.0
C6 D:52B701 3.8 29.3 1.0
C D:MET508 4.1 25.4 1.0
CG2 D:VAL509 4.1 25.2 1.0
N D:VAL509 4.1 25.4 1.0
CG D:MET508 4.1 24.8 1.0
CL2 D:52B701 4.4 35.3 1.0
CB D:VAL509 4.4 25.4 1.0
C2 D:52B701 4.4 30.5 1.0
O12 D:52B701 4.4 23.2 1.0
CZ2 D:TRP373 4.5 20.8 1.0
C3 D:52B701 4.5 28.7 1.0
C10 D:52B701 4.6 25.8 1.0
C7 D:52B701 4.6 26.5 1.0
CA D:GLY512 4.6 24.5 1.0
CZ D:PHE504 4.7 24.3 1.0
CH2 D:TRP373 4.7 20.3 1.0
O D:VAL509 4.7 25.9 1.0
C D:VAL509 4.7 25.8 1.0
CG1 D:VAL509 4.7 25.3 1.0
CG D:PHE504 4.8 26.2 1.0
N D:ALA513 4.9 24.2 1.0
CB D:MET508 4.9 25.3 1.0
C D:GLY512 4.9 24.5 1.0

Reference:

J.L.Wang, D.Limburg, M.J.Graneto, J.Springer, J.R.Hamper, S.Liao, J.L.Pawlitz, R.G.Kurumbail, T.Maziasz, J.J.Talley, J.R.Kiefer, J.Carter. The Novel Benzopyran Class of Selective Cyclooxygenase-2 Inhibitors. Part 2: the Second Clinical Candidate Having A Shorter and Favorable Human Half-Life. Bioorg.Med.Chem.Lett. V. 20 7159 2010.
ISSN: ISSN 0960-894X
PubMed: 20709553
DOI: 10.1016/J.BMCL.2010.07.054
Page generated: Wed Jul 31 20:31:40 2024

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