Fluorine in PDB 7se9: Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak

The structure of Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak, PDB code: 7se9 was solved by Y.Shi, I.M.El-Deeb, V.Masic, L.Hartley-Tassell, A.Maggioni, M.Vonitzstein, T.Ve, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.88 / 1.75
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	67.605, 138.548, 68.967, 90, 90, 90
R / Rfree (%)	18.7 / 22.2

The binding sites of Fluorine atom in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak (pdb code 7se9). 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 Human Fibrillarin in Complex with Compound 1 From Single Soak, PDB code: 7se9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak


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 Human Fibrillarin in Complex with Compound 1 From Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:49.7 occ:1.00 F1 A:8W1401 0.0 49.7 1.0 C9 A:8W1401 1.3 54.6 1.0 F3 A:8W1401 2.2 48.0 1.0 F2 A:8W1401 2.2 61.9 1.0 C5 A:8W1401 2.4 37.9 1.0 HB3 A:LEU166 2.6 22.6 1.0 HD13 A:LEU166 2.7 26.6 1.0 HG22 A:ILE245 2.8 32.2 1.0 H6 A:8W1401 2.9 62.4 1.0 C6 A:8W1401 3.1 52.0 1.0 HB3 A:ALA217 3.2 28.0 1.0 HB1 A:ALA217 3.2 28.0 1.0 CB A:LEU166 3.4 18.8 1.0 HB2 A:LEU166 3.4 22.6 1.0 CD1 A:LEU166 3.5 22.2 1.0 HD12 A:LEU166 3.5 26.6 1.0 CB A:ALA217 3.6 23.4 1.0 CG2 A:ILE245 3.6 26.8 1.0 HG21 A:ILE245 3.6 32.2 1.0 C4 A:8W1401 3.6 41.6 1.0 HG22 A:VAL246 3.7 25.2 1.0 HB2 A:ALA217 3.8 28.0 1.0 H5 A:8W1401 3.8 49.9 1.0 HB A:ILE245 3.9 31.3 1.0 HD22 A:LEU166 3.9 18.0 1.0 CG A:LEU166 4.0 16.7 1.0 HG23 A:VAL246 4.0 25.2 1.0 HD11 A:LEU166 4.3 26.6 1.0 H A:FMT402 4.3 60.8 1.0 HG23 A:ILE245 4.3 32.2 1.0 CG2 A:VAL246 4.3 21.0 1.0 HB1 A:ALA235 4.3 20.4 1.0 CB A:ILE245 4.3 26.1 1.0 C7 A:8W1401 4.4 52.8 1.0 HA A:VAL246 4.4 18.1 1.0 CD2 A:LEU166 4.5 15.0 1.0 CA A:LEU166 4.6 16.9 1.0 N1 A:8W1401 4.6 60.0 1.0 N A:VAL246 4.7 16.2 1.0 H A:VAL246 4.7 19.4 1.0 C A:LEU166 4.7 17.8 1.0 HG2 A:GLN242 4.7 49.0 1.0 HB3 A:GLN242 4.8 46.2 1.0 HA A:LEU166 4.8 20.3 1.0 HB2 A:ALA235 4.8 20.4 1.0 HG A:LEU166 4.8 20.0 1.0 C A:ILE245 4.9 17.3 1.0 HG21 A:VAL246 4.9 25.2 1.0 O A:LEU166 5.0 19.2 1.0 O A:GLN242 5.0 18.9 1.0 HD22 A:ASN249 5.0 20.2 1.0 CA A:ALA217 5.0 18.1 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak


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 Human Fibrillarin in Complex with Compound 1 From Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:61.9 occ:1.00 F2 A:8W1401 0.0 61.9 1.0 C9 A:8W1401 1.4 54.6 1.0 F3 A:8W1401 2.2 48.0 1.0 F1 A:8W1401 2.2 49.7 1.0 C5 A:8W1401 2.3 37.9 1.0 H5 A:8W1401 2.7 49.9 1.0 C4 A:8W1401 2.8 41.6 1.0 HB3 A:GLN242 3.0 46.2 1.0 HG22 A:VAL237 3.1 40.9 1.0 HG23 A:VAL246 3.2 25.2 1.0 HB1 A:ALA235 3.3 20.4 1.0 HG22 A:VAL246 3.4 25.2 1.0 HG23 A:VAL237 3.6 40.9 1.0 HA A:VAL237 3.7 56.9 1.0 CG2 A:VAL246 3.7 21.0 1.0 C6 A:8W1401 3.7 52.0 1.0 O A:ASP236 3.8 37.8 1.0 CG2 A:VAL237 3.8 34.1 1.0 HG2 A:GLN242 3.8 49.0 1.0 CB A:GLN242 3.9 38.5 1.0 HG21 A:VAL246 3.9 25.2 1.0 HB3 A:LEU166 4.0 22.6 1.0 O A:GLN242 4.0 18.9 1.0 H6 A:8W1401 4.0 62.4 1.0 OE1 A:GLN242 4.1 38.4 1.0 HB A:ILE245 4.1 31.3 1.0 HB2 A:LEU166 4.1 22.6 1.0 HG22 A:ILE245 4.2 32.2 1.0 CG A:GLN242 4.2 40.9 1.0 CB A:ALA235 4.2 17.0 1.0 N1 A:8W1401 4.2 60.0 1.0 C A:ASP236 4.4 45.6 1.0 HD13 A:LEU166 4.4 26.6 1.0 CD A:GLN242 4.4 45.2 1.0 HG21 A:VAL237 4.4 40.9 1.0 HB2 A:ALA235 4.4 20.4 1.0 CA A:VAL237 4.4 47.4 1.0 HD12 A:LEU166 4.5 26.6 1.0 HA A:GLN242 4.5 35.3 1.0 CB A:LEU166 4.5 18.8 1.0 HB2 A:GLN242 4.5 46.2 1.0 H A:VAL246 4.6 19.4 1.0 C A:GLN242 4.6 28.1 1.0 H A:ASP236 4.6 21.5 1.0 CA A:GLN242 4.6 29.4 1.0 N A:VAL237 4.7 34.8 1.0 C7 A:8W1401 4.7 52.8 1.0 HB3 A:ALA235 4.7 20.4 1.0 CB A:VAL237 4.8 38.2 1.0 CG2 A:ILE245 4.8 26.8 1.0 HG21 A:ILE245 4.9 32.2 1.0 CD1 A:LEU166 4.9 22.2 1.0 N A:ASP236 4.9 17.9 1.0 CB A:ILE245 4.9 26.1 1.0 N A:VAL246 4.9 16.2 1.0 O A:LEU166 5.0 19.2 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak


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 Human Fibrillarin in Complex with Compound 1 From Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:48.0 occ:1.00 F3 A:8W1401 0.0 48.0 1.0 C9 A:8W1401 1.4 54.6 1.0 F1 A:8W1401 2.2 49.7 1.0 F2 A:8W1401 2.2 61.9 1.0 C5 A:8W1401 2.4 37.9 1.0 HG2 A:GLN242 2.6 49.0 1.0 HB A:ILE245 3.0 31.3 1.0 HG22 A:ILE245 3.1 32.2 1.0 HG21 A:ILE245 3.1 32.2 1.0 C6 A:8W1401 3.2 52.0 1.0 HB3 A:GLN242 3.3 46.2 1.0 H A:FMT402 3.3 60.8 1.0 CG2 A:ILE245 3.4 26.8 1.0 CG A:GLN242 3.4 40.9 1.0 H6 A:8W1401 3.4 62.4 1.0 C4 A:8W1401 3.4 41.6 1.0 CB A:ILE245 3.6 26.1 1.0 HA A:GLN242 3.7 35.3 1.0 CB A:GLN242 3.7 38.5 1.0 HG13 A:ILE245 3.7 38.7 1.0 HB3 A:ALA217 3.8 28.0 1.0 H5 A:8W1401 3.8 49.9 1.0 CD A:GLN242 3.9 45.2 1.0 C A:FMT402 4.0 50.7 1.0 O2 A:FMT402 4.0 57.2 1.0 CG1 A:ILE245 4.1 32.2 1.0 HG12 A:ILE245 4.1 38.7 1.0 HG3 A:GLN242 4.1 49.0 1.0 OE1 A:GLN242 4.2 38.4 1.0 CA A:GLN242 4.2 29.4 1.0 HO2 A:FMT402 4.2 68.7 1.0 O A:GLN242 4.3 18.9 1.0 HG23 A:ILE245 4.3 32.2 1.0 HG23 A:VAL246 4.3 25.2 1.0 C7 A:8W1401 4.4 52.8 1.0 HB1 A:ALA217 4.5 28.0 1.0 NE2 A:GLN242 4.5 37.2 1.0 N1 A:8W1401 4.5 60.0 1.0 HG22 A:VAL237 4.5 40.9 1.0 CB A:ALA217 4.6 23.4 1.0 HE21 A:GLN242 4.6 44.7 1.0 HB2 A:GLN242 4.6 46.2 1.0 HB3 A:LEU166 4.7 22.6 1.0 C A:GLN242 4.7 28.1 1.0 H A:VAL246 4.7 19.4 1.0 HD13 A:LEU166 4.8 26.6 1.0 HG22 A:VAL246 4.8 25.2 1.0 CA A:ILE245 4.9 18.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak


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 Human Fibrillarin in Complex with Compound 1 From Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:26.8 occ:1.00 F1 B:8W1401 0.0 26.8 1.0 C9 B:8W1401 1.4 41.0 1.0 F2 B:8W1401 2.2 33.6 1.0 F3 B:8W1401 2.3 31.2 1.0 C5 B:8W1401 2.4 26.0 1.0 HB3 B:LEU166 2.5 22.2 1.0 HG21 B:ILE245 2.6 29.7 1.0 HD13 B:LEU166 2.6 25.1 1.0 HB3 B:ALA217 3.0 21.4 1.0 C6 B:8W1401 3.0 33.5 1.0 HB1 B:ALA217 3.1 21.4 1.0 H6 B:8W1401 3.1 40.2 1.0 CB B:LEU166 3.3 18.5 1.0 HB2 B:LEU166 3.3 22.2 1.0 CB B:ALA217 3.4 17.8 1.0 CD1 B:LEU166 3.4 20.9 1.0 CG2 B:ILE245 3.5 24.8 1.0 HG22 B:VAL246 3.6 25.6 1.0 HB2 B:ALA217 3.6 21.4 1.0 HD12 B:LEU166 3.6 25.1 1.0 C4 B:8W1401 3.6 27.6 1.0 HG23 B:ILE245 3.7 29.7 1.0 HD22 B:LEU166 3.8 18.2 1.0 CG B:LEU166 3.9 17.9 1.0 H5 B:8W1401 3.9 33.1 1.0 HB B:ILE245 3.9 25.5 1.0 HG23 B:VAL246 4.0 25.6 1.0 HG22 B:ILE245 4.1 29.7 1.0 HD11 B:LEU166 4.2 25.1 1.0 CG2 B:VAL246 4.3 21.3 1.0 HA B:VAL246 4.3 22.8 1.0 CB B:ILE245 4.3 21.3 1.0 C7 B:8W1401 4.4 36.0 1.0 CD2 B:LEU166 4.4 15.2 1.0 CA B:LEU166 4.5 15.8 1.0 HB1 B:ALA235 4.5 17.6 1.0 HB3 B:GLN242 4.6 35.0 1.0 N1 B:8W1401 4.6 31.1 1.0 N B:VAL246 4.6 16.8 1.0 H B:VAL246 4.7 20.2 1.0 HA B:LEU166 4.7 18.9 1.0 HG2 B:GLN242 4.7 39.5 1.0 C B:LEU166 4.7 15.2 1.0 C B:ILE245 4.8 18.1 1.0 HD12 B:ILE245 4.8 42.7 1.0 HG B:LEU166 4.8 21.5 1.0 HD22 B:ASN249 4.8 22.3 1.0 HD21 B:ASN249 4.8 22.3 1.0 HB2 B:ALA235 4.8 17.6 1.0 HD21 B:LEU166 4.8 18.2 1.0 CA B:ALA217 4.8 17.8 1.0 H B:FMT402 4.9 42.6 1.0 CA B:VAL246 4.9 19.0 1.0 HG21 B:VAL246 4.9 25.6 1.0 ND2 B:ASN249 4.9 18.6 1.0 O B:GLN242 4.9 22.5 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak


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 Human Fibrillarin in Complex with Compound 1 From Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:33.6 occ:1.00 F2 B:8W1401 0.0 33.6 1.0 C9 B:8W1401 1.4 41.0 1.0 F1 B:8W1401 2.2 26.8 1.0 F3 B:8W1401 2.3 31.2 1.0 C5 B:8W1401 2.3 26.0 1.0 H5 B:8W1401 2.7 33.1 1.0 HB3 B:GLN242 2.7 35.0 1.0 C4 B:8W1401 2.9 27.6 1.0 HG23 B:VAL246 2.9 25.6 1.0 HG22 B:VAL246 3.0 25.6 1.0 HG22 B:VAL237 3.3 33.8 1.0 CG2 B:VAL246 3.3 21.3 1.0 HB1 B:ALA235 3.4 17.6 1.0 CB B:GLN242 3.6 29.2 1.0 C6 B:8W1401 3.7 33.5 1.0 HG21 B:VAL246 3.7 25.6 1.0 O B:GLN242 3.7 22.5 1.0 HG2 B:GLN242 3.7 39.5 1.0 HG21 B:ILE245 3.8 29.7 1.0 HB3 B:LEU166 3.9 22.2 1.0 HB B:ILE245 3.9 25.5 1.0 HB2 B:LEU166 4.0 22.2 1.0 HG23 B:VAL237 4.0 33.8 1.0 CG B:GLN242 4.0 33.0 1.0 H6 B:8W1401 4.1 40.2 1.0 CG2 B:VAL237 4.1 28.1 1.0 HD13 B:LEU166 4.1 25.1 1.0 HA B:VAL237 4.1 31.9 1.0 HA B:GLN242 4.2 35.9 1.0 OE1 B:GLN242 4.2 34.6 1.0 CD B:GLN242 4.2 27.4 1.0 H B:VAL246 4.2 20.2 1.0 N1 B:8W1401 4.2 31.1 1.0 HB2 B:GLN242 4.3 35.0 1.0 CB B:ALA235 4.3 14.7 1.0 CA B:GLN242 4.3 29.9 1.0 C B:GLN242 4.3 22.8 1.0 HB2 B:ALA235 4.3 17.6 1.0 HD12 B:LEU166 4.4 25.1 1.0 O B:ASP236 4.4 25.0 1.0 CB B:LEU166 4.4 18.5 1.0 N B:VAL246 4.6 16.8 1.0 CG2 B:ILE245 4.6 24.8 1.0 HG21 B:VAL237 4.6 33.8 1.0 C7 B:8W1401 4.7 36.0 1.0 CD1 B:LEU166 4.7 20.9 1.0 CB B:ILE245 4.7 21.3 1.0 CB B:VAL246 4.7 16.9 1.0 HA B:VAL246 4.7 22.8 1.0 H B:ASP236 4.8 20.3 1.0 HB3 B:ALA235 4.8 17.6 1.0 CA B:VAL237 4.9 26.5 1.0 HD11 B:ILE245 4.9 42.7 1.0 C B:ASP236 4.9 26.7 1.0 HG23 B:ILE245 4.9 29.7 1.0 CA B:VAL246 4.9 19.0 1.0 HB3 B:ALA217 4.9 21.4 1.0 NE2 B:GLN242 5.0 33.3 1.0 HG3 B:GLN242 5.0 39.5 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Human Fibrillarin in Complex with Compound 1 From Single Soak


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 Human Fibrillarin in Complex with Compound 1 From Single Soak within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:31.2 occ:1.00 F3 B:8W1401 0.0 31.2 1.0 C9 B:8W1401 1.4 41.0 1.0 F2 B:8W1401 2.3 33.6 1.0 F1 B:8W1401 2.3 26.8 1.0 C5 B:8W1401 2.3 26.0 1.0 HG2 B:GLN242 2.5 39.5 1.0 HG21 B:ILE245 2.7 29.7 1.0 HB B:ILE245 2.8 25.5 1.0 H6 B:8W1401 3.0 40.2 1.0 HD12 B:ILE245 3.0 42.7 1.0 HD11 B:ILE245 3.1 42.7 1.0 HB3 B:GLN242 3.1 35.0 1.0 HG23 B:ILE245 3.1 29.7 1.0 C6 B:8W1401 3.2 33.5 1.0 CG2 B:ILE245 3.2 24.8 1.0 CG B:GLN242 3.3 33.0 1.0 CB B:ILE245 3.4 21.3 1.0 HA B:GLN242 3.4 35.9 1.0 C4 B:8W1401 3.4 27.6 1.0 CD1 B:ILE245 3.5 35.6 1.0 HB3 B:ALA217 3.5 21.4 1.0 CB B:GLN242 3.6 29.2 1.0 H5 B:8W1401 3.8 33.1 1.0 CD B:GLN242 3.8 27.4 1.0 H B:FMT402 3.9 42.6 1.0 CA B:GLN242 4.0 29.9 1.0 CG1 B:ILE245 4.0 29.2 1.0 HE21 B:GLN242 4.1 39.9 1.0 O B:GLN242 4.1 22.5 1.0 HG3 B:GLN242 4.1 39.5 1.0 HG22 B:ILE245 4.1 29.7 1.0 NE2 B:GLN242 4.2 33.3 1.0 C B:FMT402 4.2 35.5 1.0 HB1 B:ALA217 4.3 21.4 1.0 HG23 B:VAL246 4.3 25.6 1.0 CB B:ALA217 4.3 17.8 1.0 O1 B:FMT402 4.3 48.1 1.0 HD13 B:ILE245 4.3 42.7 1.0 C7 B:8W1401 4.4 36.0 1.0 OE1 B:GLN242 4.5 34.6 1.0 N1 B:8W1401 4.5 31.1 1.0 HB2 B:GLN242 4.5 35.0 1.0 C B:GLN242 4.5 22.8 1.0 H B:VAL246 4.6 20.2 1.0 HG22 B:VAL246 4.6 25.6 1.0 HG12 B:ILE245 4.6 35.0 1.0 HB3 B:LEU166 4.7 22.2 1.0 HG13 B:ILE245 4.7 35.0 1.0 HD13 B:LEU166 4.7 25.1 1.0 CA B:ILE245 4.7 17.8 1.0 HB2 B:ALA217 4.7 21.4 1.0 HE22 B:GLN242 4.8 39.9 1.0 N B:VAL246 4.8 16.8 1.0 C B:ILE245 4.9 18.1 1.0 CG2 B:VAL246 4.9 21.3 1.0 HG22 B:VAL237 5.0 33.8 1.0

Y.Shi, I.M.El-Deeb, V.Masic, L.Hartley-Tassell, A.Maggioni, M.V.Itzstein, T.Ve. Discovery of Cofactor Competitive Inhibitors Against the Human Methyltransferase Fibrillarin. Pharmaceuticals V. 15 2021.
ISSN: ESSN 1424-8247
PubMed: 35056083
DOI: 10.3390/PH15010026