Fluorine in PDB 6afe: Dj-1 with Compound 7

All present enzymatic activity of Dj-1 with Compound 7:
3.5.1.124;

The structure of Dj-1 with Compound 7, PDB code: 6afe was solved by J.M.M.Caaveiro, S.Tashiro, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	75.410, 75.410, 75.210, 90.00, 90.00, 120.00
R / Rfree (%)	11.6 / 14.6

The structure of Dj-1 with Compound 7 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Dj-1 with Compound 7 (pdb code 6afe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Dj-1 with Compound 7, PDB code: 6afe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Dj-1 with Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Dj-1 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:28.7 occ:0.60 F13 A:72T201 0.0 28.7 0.6 C10 A:72T201 1.3 27.1 0.6 F14 A:72T201 2.0 29.2 0.6 F15 A:72T201 2.1 28.1 0.6 C5 A:72T201 2.3 20.3 0.6 ND2 A:ASN76 2.9 27.3 1.0 C6 A:72T201 2.9 16.2 0.6 O A:HOH302 3.1 34.5 0.4 O A:HOH303 3.1 33.7 0.4 N7 A:72T201 3.1 20.7 0.6 CG A:ASN76 3.2 26.3 1.0 C4 A:72T201 3.3 18.6 0.6 OD1 A:ASN76 3.3 26.1 1.0 O A:HOH436 3.5 24.0 1.0 O A:HOH457 3.8 44.8 1.0 CL A:CL203 4.1 32.0 1.0 C1 A:72T201 4.2 18.0 0.6 CB A:ASN76 4.2 16.4 1.0 C8 A:72T201 4.4 18.0 0.6 C3 A:72T201 4.5 20.0 0.6 C2 A:72T201 4.8 19.7 0.6 C9 A:72T201 5.0 23.3 0.6

Fluorine binding site 2 out of 6 in the Dj-1 with Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Dj-1 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:29.2 occ:0.60 F14 A:72T201 0.0 29.2 0.6 C10 A:72T201 1.2 27.1 0.6 O A:HOH302 1.6 34.5 0.4 F13 A:72T201 2.0 28.7 0.6 F15 A:72T201 2.0 28.1 0.6 C5 A:72T201 2.2 20.3 0.6 C6 A:72T201 2.7 16.2 0.6 O A:HOH303 2.8 33.7 0.4 N7 A:72T201 2.8 20.7 0.6 C4 A:72T201 3.3 18.6 0.6 OD1 A:ASN76 3.3 26.1 1.0 O A:HOH457 3.6 44.8 1.0 CB A:LEU128 3.7 17.6 1.0 ND2 A:ASN76 3.7 27.3 1.0 CG A:ASN76 3.8 26.3 1.0 C1 A:72T201 4.0 18.0 0.6 ND1 A:HIS126 4.1 13.7 1.0 C8 A:72T201 4.1 18.0 0.6 CD1 A:LEU128 4.4 24.9 1.0 CG A:HIS126 4.4 12.1 1.0 C A:LEU128 4.4 16.1 1.0 C3 A:72T201 4.5 20.0 0.6 CA A:LEU128 4.6 16.2 1.0 CE1 A:HIS126 4.6 15.6 1.0 CG A:LEU128 4.6 21.8 1.0 O A:LEU128 4.7 20.6 1.0 N A:ALA129 4.7 13.6 1.0 C9 A:72T201 4.7 23.3 0.6 CB A:HIS126 4.7 13.7 1.0 C2 A:72T201 4.7 19.7 0.6 O11 A:72T201 4.9 15.5 0.6 O A:HOH336 5.0 36.2 0.4

Fluorine binding site 3 out of 6 in the Dj-1 with Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Dj-1 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F201 b:28.1 occ:0.60 F15 A:72T201 0.0 28.1 0.6 C10 A:72T201 1.3 27.1 0.6 F14 A:72T201 2.0 29.2 0.6 F13 A:72T201 2.1 28.7 0.6 C5 A:72T201 2.3 20.3 0.6 C4 A:72T201 2.6 18.6 0.6 CD1 A:LEU128 3.1 24.9 1.0 C6 A:72T201 3.5 16.2 0.6 CB A:LEU128 3.6 17.6 1.0 O A:HOH302 3.6 34.5 0.4 O A:HOH457 3.7 44.8 1.0 CG A:LEU128 4.0 21.8 1.0 C3 A:72T201 4.0 20.0 0.6 N7 A:72T201 4.2 20.7 0.6 O A:HOH436 4.3 24.0 1.0 O A:HOH303 4.3 33.7 0.4 CE1 A:HIS126 4.4 15.6 1.0 ND1 A:HIS126 4.5 13.7 1.0 ND2 A:ASN76 4.5 27.3 1.0 C1 A:72T201 4.6 18.0 0.6 C2 A:72T201 4.8 19.7 0.6 OD1 A:ASN76 5.0 26.1 1.0

Fluorine binding site 4 out of 6 in the Dj-1 with Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Dj-1 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:39.9 occ:1.00 F13 A:72T202 0.0 39.9 1.0 C10 A:72T202 1.4 37.4 1.0 F14 A:72T202 2.3 50.4 1.0 F15 A:72T202 2.3 42.0 1.0 C5 A:72T202 2.3 25.7 1.0 C6 A:72T202 2.9 27.7 1.0 N7 A:72T202 3.1 30.1 1.0 O A:HOH463 3.3 63.8 1.0 O A:HOH446 3.4 37.8 0.5 C4 A:72T202 3.4 29.6 1.0 O A:HOH325 3.6 26.6 1.0 O A:HOH312 3.6 35.4 1.0 O A:ALA171 3.7 24.5 1.0 CD1 A:LEU172 4.2 30.5 1.0 C1 A:72T202 4.2 28.1 1.0 C8 A:72T202 4.4 30.1 1.0 C A:ALA171 4.4 20.6 1.0 C3 A:72T202 4.6 25.0 1.0 CB A:ALA171 4.8 21.6 1.0 CB A:LEU101 4.8 16.9 1.0 C2 A:72T202 4.9 27.4 1.0 C9 A:72T202 5.0 29.1 1.0

Fluorine binding site 5 out of 6 in the Dj-1 with Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Dj-1 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:50.4 occ:1.00 F14 A:72T202 0.0 50.4 1.0 C10 A:72T202 1.4 37.4 1.0 F15 A:72T202 2.2 42.0 1.0 F13 A:72T202 2.3 39.9 1.0 C5 A:72T202 2.3 25.7 1.0 C6 A:72T202 2.9 27.7 1.0 N7 A:72T202 3.0 30.1 1.0 O A:HOH312 3.3 35.4 1.0 C4 A:72T202 3.5 29.6 1.0 C1 A:72T202 4.2 28.1 1.0 O A:HOH446 4.2 37.8 0.5 C8 A:72T202 4.3 30.1 1.0 C3 A:72T202 4.6 25.0 1.0 O A:HOH463 4.7 63.8 1.0 O A:ALA171 4.7 24.5 1.0 O A:HOH337 4.8 40.9 1.0 C2 A:72T202 4.9 27.4 1.0 C9 A:72T202 5.0 29.1 1.0

Fluorine binding site 6 out of 6 in the Dj-1 with Compound 7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Dj-1 with Compound 7 within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:42.0 occ:1.00 F15 A:72T202 0.0 42.0 1.0 C10 A:72T202 1.4 37.4 1.0 F14 A:72T202 2.2 50.4 1.0 F13 A:72T202 2.3 39.9 1.0 C5 A:72T202 2.3 25.7 1.0 C4 A:72T202 2.7 29.6 1.0 O A:HOH325 3.1 26.6 1.0 O A:HOH463 3.6 63.8 1.0 C6 A:72T202 3.6 27.7 1.0 C3 A:72T202 4.1 25.0 1.0 O A:HOH337 4.1 40.9 1.0 O A:LYS99 4.2 23.2 1.0 N7 A:72T202 4.4 30.1 1.0 O A:HOH471 4.4 53.4 1.0 O A:HOH446 4.7 37.8 0.5 C1 A:72T202 4.7 28.1 1.0 C2 A:72T202 4.9 27.4 1.0 N A:LEU101 4.9 17.9 1.0

S.Tashiro, J.M.M.Caaveiro, M.Nakakido, A.Tanabe, S.Nagatoishi, Y.Tamura, N.Matsuda, D.Liu, Q.Q.Hoang, K.Tsumoto. Discovery and Optimization of Inhibitors of the Parkinson'S Disease Associated Protein Dj-1. Acs Chem. Biol. V. 13 2783 2018.
ISSN: ESSN 1554-8937
PubMed: 30063823
DOI: 10.1021/ACSCHEMBIO.8B00701