Fluorine in PDB 7p4k: Soluble Epoxide Hydrolase in Complex with FL217

Enzymatic activity of Soluble Epoxide Hydrolase in Complex with FL217

All present enzymatic activity of Soluble Epoxide Hydrolase in Complex with FL217:
3.1.3.76; 3.3.2.10;

Protein crystallography data

The structure of Soluble Epoxide Hydrolase in Complex with FL217, PDB code: 7p4k was solved by X.Ni, J.S.Kramer, F.Lillich, E.Proschak, A.Chaikuad, S.Knapp, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.02 / 2.15
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.82, 79.326, 88.599, 90, 126.65, 90
R / Rfree (%) 17.7 / 22.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Soluble Epoxide Hydrolase in Complex with FL217 (pdb code 7p4k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Soluble Epoxide Hydrolase in Complex with FL217, PDB code: 7p4k:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 7p4k

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Fluorine binding site 1 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:47.7
occ:1.00
 F3 A:5IV601 0.0 47.7 1.0
C19 A:5IV601 1.3 46.2 1.0
F1 A:5IV601 2.1 51.1 1.0
F2 A:5IV601 2.2 46.5 1.0
C18 A:5IV601 2.3 46.8 1.0
C17 A:5IV601 3.0 42.2 1.0
C16 A:5IV601 3.1 42.9 1.0
C20 A:5IV601 3.4 44.6 1.0
OH A:TYR466 3.5 39.7 1.0
CE A:MET419 3.8 87.5 1.0
O A:5IV601 3.8 46.7 1.0
CE1 A:PHE267 4.0 34.9 1.0
CD1 A:PHE267 4.0 33.8 1.0
CE2 A:PHE387 4.1 44.8 1.0
CE2 A:TYR383 4.1 52.2 1.0
N1 A:5IV601 4.3 43.2 1.0
C26 A:5IV601 4.3 42.1 1.0
CZ A:PHE387 4.3 44.8 1.0
C A:5IV601 4.4 46.6 1.0
C21 A:5IV601 4.5 49.0 1.0
CD2 A:TYR383 4.6 56.5 1.0
CZ A:TYR466 4.7 41.9 1.0
SD A:MET419 4.8 93.5 1.0
C25 A:5IV601 4.9 41.0 1.0
CZ A:TYR383 5.0 53.9 1.0

Fluorine binding site 2 out of 8 in 7p4k

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Fluorine binding site 2 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:46.5
occ:1.00
 F2 A:5IV601 0.0 46.5 1.0
C19 A:5IV601 1.3 46.2 1.0
F1 A:5IV601 2.1 51.1 1.0
F3 A:5IV601 2.2 47.7 1.0
C18 A:5IV601 2.3 46.8 1.0
C16 A:5IV601 3.0 42.9 1.0
C17 A:5IV601 3.0 42.2 1.0
O A:PHE267 3.3 33.4 1.0
C20 A:5IV601 3.3 44.6 1.0
CD1 A:PHE267 3.4 33.8 1.0
CH2 A:TRP525 3.6 35.6 1.0
CE1 A:PHE267 3.7 34.9 1.0
CD A:PRO268 3.7 34.2 1.0
C A:PHE267 4.0 34.0 1.0
CZ2 A:TRP525 4.2 37.4 1.0
N A:PRO268 4.3 34.5 1.0
OH A:TYR466 4.3 39.7 1.0
C26 A:5IV601 4.4 42.1 1.0
N1 A:5IV601 4.4 43.2 1.0
CD2 A:LEU408 4.5 45.8 1.0
CG A:PHE267 4.6 34.0 1.0
C21 A:5IV601 4.6 49.0 1.0
CZ3 A:TRP525 4.6 37.0 1.0
CG A:PRO268 4.7 35.0 1.0
CD1 A:LEU408 4.9 44.9 1.0
CB A:PHE267 4.9 33.8 1.0
O A:5IV601 4.9 46.7 1.0
C25 A:5IV601 5.0 41.0 1.0
O A:HOH704 5.0 30.4 1.0
NE2 A:HIS524 5.0 35.9 1.0

Fluorine binding site 3 out of 8 in 7p4k

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Fluorine binding site 3 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:51.1
occ:1.00
 F1 A:5IV601 0.0 51.1 1.0
C19 A:5IV601 1.3 46.2 1.0
F2 A:5IV601 2.1 46.5 1.0
F3 A:5IV601 2.1 47.7 1.0
C18 A:5IV601 2.3 46.8 1.0
C20 A:5IV601 2.6 44.6 1.0
CD2 A:LEU408 3.2 45.8 1.0
C17 A:5IV601 3.6 42.2 1.0
C21 A:5IV601 3.9 49.0 1.0
CE A:MET419 4.1 87.5 1.0
C16 A:5IV601 4.3 42.9 1.0
CZ2 A:TRP525 4.3 37.4 1.0
CH2 A:TRP525 4.4 35.6 1.0
CG A:LEU408 4.4 43.2 1.0
O A:HOH706 4.5 63.8 1.0
SD A:MET419 4.5 93.5 1.0
CD1 A:LEU408 4.6 44.9 1.0
N2 A:5IV601 4.7 55.8 1.0
C26 A:5IV601 4.7 42.1 1.0
C25 A:5IV601 4.8 41.0 1.0
CB A:LEU408 4.9 40.4 1.0
CE1 A:PHE267 4.9 34.9 1.0
CD1 A:LEU417 4.9 83.9 1.0
CD1 A:LEU428 5.0 65.1 1.0

Fluorine binding site 4 out of 8 in 7p4k

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Fluorine binding site 4 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:78.4
occ:1.00
 F A:5IV601 0.0 78.4 1.0
C8 A:5IV601 1.4 73.8 1.0
C7 A:5IV601 2.3 65.1 1.0
C9 A:5IV601 2.3 77.9 1.0
CE A:MET503 2.6 75.8 1.0
CG A:PRO361 3.3 49.4 1.0
CD A:PRO361 3.5 45.2 1.0
C10 A:5IV601 3.6 78.6 1.0
C6 A:5IV601 3.6 66.0 1.0
CD2 A:LEU499 4.0 47.0 1.0
C11 A:5IV601 4.1 77.8 1.0
SD A:MET503 4.2 73.9 1.0
CG1 A:ILE363 4.8 62.7 1.0
CB A:PRO361 4.8 51.7 1.0
N A:PRO361 4.8 44.1 1.0
C5 A:5IV601 4.8 63.1 1.0
N A:5IV601 4.9 56.1 1.0
CB A:MET503 4.9 62.7 1.0

Fluorine binding site 5 out of 8 in 7p4k

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Fluorine binding site 5 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:52.6
occ:1.00
 F3 B:5IV601 0.0 52.6 1.0
C19 B:5IV601 1.3 52.5 1.0
F1 B:5IV601 2.1 60.5 1.0
F2 B:5IV601 2.2 53.0 1.0
C18 B:5IV601 2.4 52.4 1.0
C16 B:5IV601 3.1 46.2 1.0
C17 B:5IV601 3.1 48.1 1.0
C20 B:5IV601 3.4 52.9 1.0
CD1 B:PHE267 3.4 36.7 1.0
O B:PHE267 3.4 37.7 1.0
CH2 B:TRP525 3.6 37.9 1.0
CE1 B:PHE267 3.7 37.5 1.0
CD B:PRO268 3.7 36.6 1.0
C B:PHE267 4.1 35.7 1.0
CZ2 B:TRP525 4.2 39.1 1.0
OH B:TYR466 4.3 44.8 1.0
N B:PRO268 4.3 34.2 1.0
C26 B:5IV601 4.4 49.2 1.0
CD2 B:LEU408 4.5 44.1 1.0
N1 B:5IV601 4.5 47.7 1.0
CG B:PHE267 4.6 34.8 1.0
C21 B:5IV601 4.6 55.3 1.0
CG B:PRO268 4.7 37.1 1.0
CZ3 B:TRP525 4.7 37.7 1.0
CD1 B:LEU408 4.7 43.6 1.0
CB B:PHE267 5.0 34.6 1.0
O B:5IV601 5.0 44.8 1.0
O B:HOH704 5.0 34.2 1.0

Fluorine binding site 6 out of 8 in 7p4k

Go back to Fluorine Binding Sites List in 7p4k
Fluorine binding site 6 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:53.0
occ:1.00
 F2 B:5IV601 0.0 53.0 1.0
C19 B:5IV601 1.3 52.5 1.0
F1 B:5IV601 2.1 60.5 1.0
F3 B:5IV601 2.2 52.6 1.0
C18 B:5IV601 2.4 52.4 1.0
C17 B:5IV601 3.0 48.1 1.0
C16 B:5IV601 3.1 46.2 1.0
C20 B:5IV601 3.4 52.9 1.0
OH B:TYR466 3.5 44.8 1.0
O B:5IV601 3.7 44.8 1.0
CE2 B:TYR383 3.9 56.4 1.0
CD1 B:PHE267 4.0 36.7 1.0
CE1 B:PHE267 4.1 37.5 1.0
CE2 B:PHE387 4.2 45.1 1.0
N1 B:5IV601 4.2 47.7 1.0
C26 B:5IV601 4.2 49.2 1.0
C B:5IV601 4.3 46.7 1.0
CZ B:PHE387 4.4 46.0 1.0
C21 B:5IV601 4.5 55.3 1.0
CD2 B:TYR383 4.5 55.8 1.0
CZ B:TYR466 4.7 41.8 1.0
CZ B:TYR383 4.7 57.1 1.0
C25 B:5IV601 4.8 56.0 1.0
OH B:TYR383 4.8 54.6 1.0

Fluorine binding site 7 out of 8 in 7p4k

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Fluorine binding site 7 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:60.5
occ:1.00
 F1 B:5IV601 0.0 60.5 1.0
C19 B:5IV601 1.3 52.5 1.0
F2 B:5IV601 2.1 53.0 1.0
F3 B:5IV601 2.1 52.6 1.0
C18 B:5IV601 2.3 52.4 1.0
C20 B:5IV601 2.6 52.9 1.0
CD2 B:LEU408 3.2 44.1 1.0
C17 B:5IV601 3.6 48.1 1.0
C21 B:5IV601 3.9 55.3 1.0
C16 B:5IV601 4.3 46.2 1.0
CG B:LEU408 4.3 43.5 1.0
CZ2 B:TRP525 4.4 39.1 1.0
CH2 B:TRP525 4.5 37.9 1.0
CD1 B:LEU408 4.6 43.6 1.0
CD1 B:LEU417 4.6 80.9 1.0
N2 B:5IV601 4.6 61.3 1.0
C26 B:5IV601 4.7 49.2 1.0
CB B:LEU408 4.8 40.9 1.0
C25 B:5IV601 4.8 56.0 1.0
CD2 B:LEU428 4.9 70.8 1.0
CE1 B:PHE267 4.9 37.5 1.0

Fluorine binding site 8 out of 8 in 7p4k

Go back to Fluorine Binding Sites List in 7p4k
Fluorine binding site 8 out of 8 in the Soluble Epoxide Hydrolase in Complex with FL217


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Soluble Epoxide Hydrolase in Complex with FL217 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:65.6
occ:1.00
 F B:5IV601 0.0 65.6 1.0
C8 B:5IV601 1.4 68.7 1.0
C7 B:5IV601 2.3 64.2 1.0
C9 B:5IV601 2.3 69.1 1.0
CE B:MET503 2.8 67.8 1.0
CG B:PRO361 3.3 41.6 1.0
CD B:PRO361 3.4 40.2 1.0
C10 B:5IV601 3.6 70.1 1.0
CD2 B:LEU499 3.6 42.8 1.0
C6 B:5IV601 3.6 60.3 1.0
SD B:MET503 4.0 68.8 1.0
C11 B:5IV601 4.1 70.8 1.0
N B:PRO361 4.7 40.2 1.0
CB B:PRO361 4.8 41.4 1.0
C5 B:5IV601 4.9 57.7 1.0
CB B:MET503 4.9 56.7 1.0
N B:5IV601 4.9 52.1 1.0

Reference:

F.F.Lillich, S.Willems, X.Ni, W.Kilu, C.Borkowsky, M.Brodsky, J.S.Kramer, S.Brunst, V.Hernandez-Olmos, J.Heering, S.Schierle, R.I.Kestner, F.M.Mayser, M.Helmstadter, T.Gobel, L.Weizel, D.Namgaladze, A.Kaiser, D.Steinhilber, W.Pfeilschifter, A.S.Kahnt, A.Proschak, A.Chaikuad, S.Knapp, D.Merk, E.Proschak. Structure-Based Design of Dual Partial Peroxisome Proliferator-Activated Receptor Gamma Agonists/Soluble Epoxide Hydrolase Inhibitors. J.Med.Chem. V. 64 17259 2021.
ISSN: ISSN 0022-2623
PubMed: 34818007
DOI: 10.1021/ACS.JMEDCHEM.1C01331
Page generated: Wed Apr 5 00:33:12 2023

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