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Fluorine in PDB 5ikv: The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2

Enzymatic activity of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2

All present enzymatic activity of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2:
1.14.99.1;

Protein crystallography data

The structure of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2, PDB code: 5ikv was solved by B.J.Orlando, M.G.Malkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.01 / 2.51
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 126.918, 149.334, 184.766, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 22.4

Other elements in 5ikv:

The structure of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 (pdb code 5ikv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2, PDB code: 5ikv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5ikv

Go back to Fluorine Binding Sites List in 5ikv
Fluorine binding site 1 out of 6 in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:51.1
occ:1.00
 F1 A:FLF601 0.0 51.1 1.0
C7' A:FLF601 1.3 48.2 1.0
F3 A:FLF601 2.2 48.2 1.0
F2 A:FLF601 2.2 47.8 1.0
C3' A:FLF601 2.3 47.7 1.0
H4' A:FLF601 2.5 58.3 1.0
HE2 A:TYR355 2.7 48.9 1.0
C4' A:FLF601 2.8 48.5 1.0
HD21 A:LEU359 3.1 44.6 1.0
HD11 A:LEU359 3.2 43.7 1.0
HG11 A:VAL116 3.3 47.2 1.0
CE2 A:TYR355 3.4 41.2 1.0
C2' A:FLF601 3.5 47.0 1.0
HD22 A:LEU359 3.6 44.6 1.0
HD2 A:TYR355 3.7 49.2 1.0
HD13 A:LEU359 3.7 43.7 1.0
CD2 A:LEU359 3.7 37.6 1.0
H2' A:FLF601 3.8 56.4 1.0
HG13 A:VAL116 3.8 47.2 1.0
CD1 A:LEU359 3.9 36.6 1.0
CD2 A:TYR355 4.0 41.5 1.0
CG1 A:VAL116 4.0 37.7 1.0
HH A:TYR355 4.0 49.9 1.0
C5' A:FLF601 4.1 50.5 1.0
HB3 A:SER353 4.3 47.6 1.0
HG12 A:VAL349 4.3 41.5 1.0
HD11 A:LEU531 4.3 39.7 1.0
HH21 A:ARG120 4.4 0.5 1.0
CZ A:TYR355 4.4 42.2 1.0
HG12 A:VAL116 4.4 47.2 1.0
HG11 A:VAL349 4.4 41.5 1.0
CG A:LEU359 4.4 37.3 1.0
HB2 A:SER353 4.5 47.6 1.0
HD23 A:LEU359 4.5 44.6 1.0
OH A:TYR355 4.6 42.0 1.0
HG21 A:VAL116 4.6 49.1 1.0
HD12 A:LEU359 4.7 43.7 1.0
C1' A:FLF601 4.7 47.7 1.0
H5' A:FLF601 4.7 60.6 1.0
CG1 A:VAL349 4.8 34.6 1.0
CB A:SER353 4.8 41.2 1.0
HE A:ARG120 4.8 87.3 1.0
HE1 A:MET113 4.9 45.5 1.0
O A:HOH719 4.9 43.1 1.0
HG A:LEU359 4.9 44.4 1.0
NH2 A:ARG120 4.9 52.6 1.0
C6' A:FLF601 4.9 48.9 1.0
HD21 A:LEU531 4.9 38.3 1.0

Fluorine binding site 2 out of 6 in 5ikv

Go back to Fluorine Binding Sites List in 5ikv
Fluorine binding site 2 out of 6 in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:47.8
occ:1.00
 F2 A:FLF601 0.0 47.8 1.0
C7' A:FLF601 1.3 48.2 1.0
F3 A:FLF601 2.2 48.2 1.0
F1 A:FLF601 2.2 51.1 1.0
C3' A:FLF601 2.3 47.7 1.0
HD11 A:LEU531 2.6 39.7 1.0
HG13 A:VAL116 3.0 47.2 1.0
C2' A:FLF601 3.2 47.0 1.0
C4' A:FLF601 3.2 48.5 1.0
HG11 A:VAL116 3.2 47.2 1.0
H2' A:FLF601 3.2 56.4 1.0
HB1 A:ALA527 3.2 42.5 1.0
H4' A:FLF601 3.3 58.3 1.0
HE A:ARG120 3.3 87.3 1.0
CG1 A:VAL116 3.4 37.7 1.0
HG12 A:VAL116 3.5 47.2 1.0
HG3 A:ARG120 3.5 57.0 1.0
CD1 A:LEU531 3.6 33.2 1.0
NE A:ARG120 3.6 49.1 1.0
HH21 A:ARG120 3.7 0.5 1.0
HD12 A:LEU531 3.8 39.7 1.0
HD13 A:LEU531 4.0 39.7 1.0
NH2 A:ARG120 4.0 52.6 1.0
CZ A:ARG120 4.0 52.0 1.0
CB A:ALA527 4.1 35.5 1.0
HE2 A:TYR355 4.2 48.9 1.0
HB2 A:ALA527 4.2 42.5 1.0
HD21 A:LEU531 4.2 38.3 1.0
HD2 A:ARG120 4.3 72.5 1.0
CD A:ARG120 4.4 46.5 1.0
CG A:ARG120 4.4 42.9 1.0
C1' A:FLF601 4.4 47.7 1.0
HB3 A:ALA527 4.4 42.5 1.0
C5' A:FLF601 4.4 50.5 1.0
O A:HOH719 4.5 43.1 1.0
HG A:LEU531 4.5 38.5 1.0
CG A:LEU531 4.6 32.0 1.0
HH A:TYR355 4.6 49.9 1.0
HH22 A:ARG120 4.6 0.5 1.0
CD2 A:LEU531 4.8 31.9 1.0
HG11 A:VAL349 4.9 41.5 1.0
CB A:VAL116 4.9 38.1 1.0
C6' A:FLF601 4.9 48.9 1.0
HG2 A:ARG120 4.9 57.0 1.0
NH1 A:ARG120 5.0 53.6 1.0
HD21 A:LEU359 5.0 44.6 1.0

Fluorine binding site 3 out of 6 in 5ikv

Go back to Fluorine Binding Sites List in 5ikv
Fluorine binding site 3 out of 6 in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:48.2
occ:1.00
 F3 A:FLF601 0.0 48.2 1.0
C7' A:FLF601 1.3 48.2 1.0
F1 A:FLF601 2.2 51.1 1.0
F2 A:FLF601 2.2 47.8 1.0
C3' A:FLF601 2.3 47.7 1.0
H2' A:FLF601 2.4 56.4 1.0
C2' A:FLF601 2.7 47.0 1.0
HD21 A:LEU531 2.9 38.3 1.0
HD11 A:LEU531 2.9 39.7 1.0
HG11 A:VAL349 3.0 41.5 1.0
HD13 A:LEU359 3.4 43.7 1.0
C4' A:FLF601 3.6 48.5 1.0
HG12 A:VAL349 3.6 41.5 1.0
HG11 A:VAL116 3.6 47.2 1.0
CG1 A:VAL349 3.7 34.6 1.0
HD11 A:LEU359 3.7 43.7 1.0
CD2 A:LEU531 3.8 31.9 1.0
CD1 A:LEU531 3.8 33.2 1.0
H4' A:FLF601 3.9 58.3 1.0
HD22 A:LEU359 3.9 44.6 1.0
CD1 A:LEU359 4.0 36.6 1.0
HG A:LEU531 4.0 38.5 1.0
HG13 A:VAL349 4.0 41.5 1.0
C1' A:FLF601 4.1 47.7 1.0
CG A:LEU531 4.1 32.0 1.0
HG12 A:VAL116 4.2 47.2 1.0
HE1 A:MET113 4.2 45.5 1.0
CG1 A:VAL116 4.2 37.7 1.0
HD21 A:LEU359 4.2 44.6 1.0
HD22 A:LEU531 4.2 38.3 1.0
HD13 A:LEU531 4.2 39.7 1.0
HB1 A:ALA527 4.3 42.5 1.0
HG13 A:VAL116 4.3 47.2 1.0
HD23 A:LEU531 4.4 38.3 1.0
HD12 A:LEU531 4.4 39.7 1.0
CD2 A:LEU359 4.5 37.6 1.0
HN1 A:FLF601 4.7 57.4 1.0
C5' A:FLF601 4.7 50.5 1.0
HD12 A:LEU359 4.7 43.7 1.0
HE2 A:TYR355 4.8 48.9 1.0
N A:FLF601 4.9 47.8 1.0
CG A:LEU359 4.9 37.3 1.0
C6' A:FLF601 4.9 48.9 1.0
CB A:VAL349 5.0 33.9 1.0
HB A:VAL349 5.0 40.8 1.0

Fluorine binding site 4 out of 6 in 5ikv

Go back to Fluorine Binding Sites List in 5ikv
Fluorine binding site 4 out of 6 in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:40.4
occ:1.00
 F1 B:FLF601 0.0 40.4 1.0
C7' B:FLF601 1.3 36.4 1.0
F2 B:FLF601 2.0 41.2 1.0
F3 B:FLF601 2.1 34.9 1.0
C3' B:FLF601 2.3 34.2 1.0
H4' B:FLF601 2.4 38.6 1.0
C4' B:FLF601 2.7 32.1 1.0
HE2 B:TYR355 2.7 40.2 1.0
HD21 B:LEU359 3.3 39.2 1.0
HG11 B:VAL116 3.4 40.0 1.0
CE2 B:TYR355 3.5 33.7 1.0
C2' B:FLF601 3.5 31.9 1.0
HD11 B:LEU359 3.7 38.6 1.0
H2' B:FLF601 3.8 38.3 1.0
HD22 B:LEU359 3.8 39.2 1.0
HG13 B:VAL116 3.9 40.0 1.0
HD2 B:TYR355 4.0 40.9 1.0
C5' B:FLF601 4.0 31.3 1.0
CD2 B:LEU359 4.0 32.9 1.0
O B:HOH728 4.0 42.3 1.0
HH21 B:ARG120 4.1 66.7 1.0
CG1 B:VAL116 4.1 33.5 1.0
CD2 B:TYR355 4.1 34.3 1.0
HB3 B:SER353 4.2 39.8 1.0
HD13 B:LEU359 4.2 38.6 1.0
HG12 B:VAL349 4.2 36.5 1.0
HB2 B:SER353 4.3 39.8 1.0
HD11 B:LEU531 4.3 35.0 1.0
HG11 B:VAL349 4.3 36.5 1.0
CZ B:TYR355 4.4 34.0 1.0
CD1 B:LEU359 4.4 32.3 1.0
OH B:TYR355 4.4 33.5 1.0
HG12 B:VAL116 4.5 40.0 1.0
HE B:ARG120 4.5 62.2 1.0
H5' B:FLF601 4.6 37.6 1.0
C1' B:FLF601 4.6 30.3 1.0
CG1 B:VAL349 4.6 30.5 1.0
NH2 B:ARG120 4.7 46.7 1.0
CB B:SER353 4.7 33.3 1.0
HD23 B:LEU359 4.7 39.2 1.0
HG13 B:VAL349 4.8 36.5 1.0
C6' B:FLF601 4.8 31.2 1.0
CG B:LEU359 4.8 33.1 1.0
HD21 B:LEU531 4.9 34.9 1.0
HB1 B:ALA527 4.9 35.6 1.0
HG21 B:VAL116 4.9 41.9 1.0

Fluorine binding site 5 out of 6 in 5ikv

Go back to Fluorine Binding Sites List in 5ikv
Fluorine binding site 5 out of 6 in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:41.2
occ:1.00
 F2 B:FLF601 0.0 41.2 1.0
C7' B:FLF601 1.3 36.4 1.0
F1 B:FLF601 2.0 40.4 1.0
F3 B:FLF601 2.1 34.9 1.0
C3' B:FLF601 2.3 34.2 1.0
HD11 B:LEU531 2.7 35.0 1.0
C2' B:FLF601 3.1 31.9 1.0
C4' B:FLF601 3.1 32.1 1.0
HE B:ARG120 3.1 62.2 1.0
H2' B:FLF601 3.2 38.3 1.0
H4' B:FLF601 3.2 38.6 1.0
HB1 B:ALA527 3.2 35.6 1.0
HG13 B:VAL116 3.3 40.0 1.0
HG11 B:VAL116 3.5 40.0 1.0
HH21 B:ARG120 3.6 66.7 1.0
NE B:ARG120 3.6 44.4 1.0
CD1 B:LEU531 3.6 29.0 1.0
HG3 B:ARG120 3.6 46.3 1.0
CG1 B:VAL116 3.7 33.5 1.0
HG12 B:VAL116 3.7 40.0 1.0
HD12 B:LEU531 3.8 35.0 1.0
O B:HOH728 4.0 42.3 1.0
NH2 B:ARG120 4.0 46.7 1.0
CB B:ALA527 4.0 29.6 1.0
HD21 B:LEU531 4.0 34.9 1.0
CZ B:ARG120 4.1 46.3 1.0
HD13 B:LEU531 4.1 35.0 1.0
HB2 B:ALA527 4.1 35.6 1.0
HE2 B:TYR355 4.2 40.2 1.0
C5' B:FLF601 4.3 31.3 1.0
C1' B:FLF601 4.3 30.3 1.0
HG B:LEU531 4.3 34.5 1.0
HD2 B:ARG120 4.3 53.2 1.0
CD B:ARG120 4.4 42.6 1.0
CG B:ARG120 4.4 40.2 1.0
HB3 B:ALA527 4.5 35.6 1.0
CG B:LEU531 4.5 28.3 1.0
HH22 B:ARG120 4.6 66.7 1.0
HG11 B:VAL349 4.7 36.5 1.0
CD2 B:LEU531 4.7 28.6 1.0
C6' B:FLF601 4.8 31.2 1.0

Fluorine binding site 6 out of 6 in 5ikv

Go back to Fluorine Binding Sites List in 5ikv
Fluorine binding site 6 out of 6 in the The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Structure of Flufenamic Acid Bound to Human Cyclooxygenase-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:34.9
occ:1.00
 F3 B:FLF601 0.0 34.9 1.0
C7' B:FLF601 1.3 36.4 1.0
F2 B:FLF601 2.1 41.2 1.0
F1 B:FLF601 2.1 40.4 1.0
C3' B:FLF601 2.4 34.2 1.0
H2' B:FLF601 2.6 38.3 1.0
HD21 B:LEU531 2.8 34.9 1.0
C2' B:FLF601 2.9 31.9 1.0
HD11 B:LEU531 2.9 35.0 1.0
HG11 B:VAL349 3.0 36.5 1.0
C4' B:FLF601 3.5 32.1 1.0
HG12 B:VAL349 3.6 36.5 1.0
HG11 B:VAL116 3.6 40.0 1.0
HD13 B:LEU359 3.6 38.6 1.0
CG1 B:VAL349 3.6 30.5 1.0
CD2 B:LEU531 3.8 28.6 1.0
HD22 B:LEU359 3.8 39.2 1.0
H4' B:FLF601 3.8 38.6 1.0
CD1 B:LEU531 3.8 29.0 1.0
HD11 B:LEU359 3.9 38.6 1.0
HG13 B:VAL349 3.9 36.5 1.0
HD21 B:LEU359 4.1 39.2 1.0
HG12 B:VAL116 4.1 40.0 1.0
HG B:LEU531 4.1 34.5 1.0
CG B:LEU531 4.2 28.3 1.0
CG1 B:VAL116 4.2 33.5 1.0
HD22 B:LEU531 4.2 34.9 1.0
C1' B:FLF601 4.2 30.3 1.0
CD1 B:LEU359 4.2 32.3 1.0
HG13 B:VAL116 4.2 40.0 1.0
HD13 B:LEU531 4.2 35.0 1.0
CD2 B:LEU359 4.3 32.9 1.0
HD23 B:LEU531 4.4 34.9 1.0
HB1 B:ALA527 4.4 35.6 1.0
HD12 B:LEU531 4.5 35.0 1.0
HE1 B:MET113 4.5 40.3 1.0
C5' B:FLF601 4.7 31.3 1.0
HE2 B:TYR355 4.8 40.2 1.0
HN1 B:FLF601 4.8 39.0 1.0
CG B:LEU359 4.9 33.1 1.0
C6' B:FLF601 4.9 31.2 1.0
CB B:VAL349 5.0 30.5 1.0

Reference:

B.J.Orlando, M.G.Malkowski. Substrate-Selective Inhibition of Cyclooxygeanse-2 By Fenamic Acid Derivatives Is Dependent on Peroxide Tone. J.Biol.Chem. V. 291 15069 2016.
ISSN: ESSN 1083-351X
PubMed: 27226593
DOI: 10.1074/JBC.M116.725713
Page generated: Thu Aug 1 10:16:19 2024

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