Fluorine in PDB 7sec: Crystal Structure of Human Fibrillarin in Complex with Compound 1A

The structure of Crystal Structure of Human Fibrillarin in Complex with Compound 1A, PDB code: 7sec 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)	48.30 / 1.90
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	68.384, 68.874, 136.436, 90, 90, 90
R / Rfree (%)	22.3 / 26.6

The binding sites of Fluorine atom in the Crystal Structure of Human Fibrillarin in Complex with Compound 1A (pdb code 7sec). 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 1A, PDB code: 7sec:
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 1A


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:44.6 occ:1.00 F A:8WP402 0.0 44.6 1.0 C8 A:8WP402 1.3 37.0 1.0 F1 A:8WP402 2.1 38.9 1.0 F2 A:8WP402 2.2 44.1 1.0 C4 A:8WP402 2.3 37.9 1.0 HB3 A:GLN242 2.9 28.8 1.0 N2 A:8WP402 3.0 33.3 1.0 HG2 A:GLN242 3.1 33.2 1.0 HG22 A:ILE245 3.1 25.5 1.0 HG21 A:ILE245 3.3 25.5 1.0 HB A:ILE245 3.3 25.4 1.0 C5 A:8WP402 3.4 47.0 1.0 CG2 A:ILE245 3.5 21.2 1.0 HA A:GLN242 3.5 39.9 1.0 CB A:GLN242 3.6 24.0 1.0 CG A:GLN242 3.6 27.7 1.0 CD A:GLN242 3.7 28.8 1.0 HG23 A:VAL246 3.8 36.3 1.0 H5 A:8WP402 3.8 56.4 1.0 HD12 A:ILE245 3.9 43.9 1.0 OE1 A:GLN242 3.9 26.1 1.0 CB A:ILE245 3.9 21.2 1.0 HD13 A:ILE245 3.9 43.9 1.0 CA A:GLN242 4.0 33.2 1.0 O A:GLN242 4.1 23.6 1.0 N1 A:8WP402 4.1 33.4 1.0 O2 A:FMT405 4.1 60.8 1.0 NE2 A:GLN242 4.2 34.4 1.0 HB3 A:ALA217 4.3 33.7 1.0 CD1 A:ILE245 4.3 36.5 1.0 H A:FMT405 4.3 66.2 1.0 C6 A:8WP402 4.4 36.0 1.0 HB2 A:GLN242 4.4 28.8 1.0 HE21 A:GLN242 4.4 41.3 1.0 HG23 A:ILE245 4.5 25.5 1.0 C A:FMT405 4.5 55.2 1.0 O A:HOH502 4.5 26.9 1.0 HG3 A:GLN242 4.5 33.2 1.0 C A:GLN242 4.5 24.4 1.0 CG2 A:VAL246 4.6 30.2 1.0 HG22 A:VAL246 4.6 36.3 1.0 HB3 A:LEU166 4.6 26.9 1.0 H A:VAL246 4.6 24.1 1.0 HO2 A:FMT405 4.6 72.9 1.0 HE22 A:GLN242 4.7 41.3 1.0 HD13 A:LEU166 4.7 34.3 1.0 CG1 A:ILE245 4.7 24.8 1.0 HG22 A:VAL237 4.8 36.7 1.0 N A:VAL246 4.9 20.1 1.0 HG21 A:VAL246 4.9 36.3 1.0 HB1 A:ALA235 4.9 27.9 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:38.9 occ:1.00 F1 A:8WP402 0.0 38.9 1.0 C8 A:8WP402 1.3 37.0 1.0 F A:8WP402 2.1 44.6 1.0 F2 A:8WP402 2.1 44.1 1.0 C4 A:8WP402 2.3 37.9 1.0 HB3 A:LEU166 2.6 26.9 1.0 H5 A:8WP402 2.8 56.4 1.0 C5 A:8WP402 2.9 47.0 1.0 HD13 A:LEU166 3.0 34.3 1.0 HB2 A:LEU166 3.2 26.9 1.0 HG22 A:ILE245 3.2 25.5 1.0 CB A:LEU166 3.3 22.4 1.0 HG23 A:VAL246 3.5 36.3 1.0 N2 A:8WP402 3.5 33.3 1.0 HG22 A:VAL246 3.6 36.3 1.0 HD12 A:LEU166 3.6 34.3 1.0 HB1 A:ALA235 3.7 27.9 1.0 CD1 A:LEU166 3.7 28.6 1.0 HB3 A:ALA217 3.9 33.7 1.0 CG2 A:VAL246 4.0 30.2 1.0 HG21 A:ILE245 4.0 25.5 1.0 CG2 A:ILE245 4.1 21.2 1.0 CG A:LEU166 4.1 24.6 1.0 C6 A:8WP402 4.2 36.0 1.0 HB1 A:ALA217 4.2 33.7 1.0 HB2 A:ALA235 4.2 27.9 1.0 HB3 A:GLN242 4.4 28.8 1.0 CB A:ALA217 4.4 28.1 1.0 CB A:ALA235 4.4 23.3 1.0 C A:LEU166 4.4 22.9 1.0 HD22 A:LEU166 4.4 26.0 1.0 N1 A:8WP402 4.4 33.4 1.0 HB A:ILE245 4.4 25.4 1.0 CA A:LEU166 4.5 25.1 1.0 HB2 A:ALA217 4.5 33.7 1.0 HA A:VAL246 4.5 29.1 1.0 HD11 A:LEU166 4.6 34.3 1.0 HG21 A:VAL246 4.6 36.3 1.0 O A:LEU166 4.6 24.1 1.0 HG23 A:ILE245 4.7 25.5 1.0 N A:GLY167 4.7 30.4 1.0 H A:VAL246 4.8 24.1 1.0 N A:VAL246 4.8 20.1 1.0 HA A:LEU166 4.8 30.1 1.0 HG A:LEU166 4.9 29.5 1.0 CD2 A:LEU166 4.9 21.7 1.0 CB A:ILE245 4.9 21.2 1.0 H A:GLY167 4.9 36.5 1.0 O A:GLN242 4.9 23.6 1.0 H A:FMT405 5.0 66.2 1.0 HB3 A:ALA235 5.0 27.9 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:44.1 occ:1.00 F2 A:8WP402 0.0 44.1 1.0 C8 A:8WP402 1.3 37.0 1.0 F1 A:8WP402 2.1 38.9 1.0 F A:8WP402 2.2 44.6 1.0 C4 A:8WP402 2.3 37.9 1.0 N2 A:8WP402 2.8 33.3 1.0 HB3 A:GLN242 3.1 28.8 1.0 HB1 A:ALA235 3.2 27.9 1.0 O A:ASP236 3.3 28.6 1.0 O A:HOH502 3.3 26.9 1.0 OE1 A:GLN242 3.5 26.1 1.0 C5 A:8WP402 3.6 47.0 1.0 HG23 A:VAL246 3.7 36.3 1.0 HA A:VAL237 3.8 28.8 1.0 HG22 A:VAL246 3.8 36.3 1.0 HG22 A:VAL237 3.9 36.7 1.0 CD A:GLN242 4.0 28.8 1.0 CB A:GLN242 4.0 24.0 1.0 N1 A:8WP402 4.0 33.4 1.0 H5 A:8WP402 4.0 56.4 1.0 C A:ASP236 4.1 32.6 1.0 O A:HOH564 4.1 39.0 1.0 CG2 A:VAL246 4.1 30.2 1.0 CB A:ALA235 4.1 23.3 1.0 H A:ASP236 4.2 24.4 1.0 HB3 A:LEU166 4.2 26.9 1.0 HG21 A:VAL246 4.2 36.3 1.0 HB2 A:LEU166 4.3 26.9 1.0 HG2 A:GLN242 4.3 33.2 1.0 CG A:GLN242 4.3 27.7 1.0 HG23 A:VAL237 4.4 36.7 1.0 HB2 A:ALA235 4.4 27.9 1.0 C6 A:8WP402 4.4 36.0 1.0 HB2 A:GLN242 4.5 28.8 1.0 N A:ASP236 4.5 20.3 1.0 HB3 A:ALA235 4.6 27.9 1.0 CG2 A:VAL237 4.6 30.6 1.0 CA A:VAL237 4.6 23.9 1.0 O A:GLN242 4.7 23.6 1.0 N A:VAL237 4.7 25.1 1.0 HG22 A:ILE245 4.7 25.5 1.0 O A:HOH520 4.7 33.4 1.0 CB A:LEU166 4.7 22.4 1.0 NE2 A:GLN242 4.7 34.4 1.0 O A:LEU166 4.8 24.1 1.0 HA A:ALA235 4.8 21.4 1.0 HA A:GLN242 4.8 39.9 1.0 HA3 A:GLY167 4.9 30.6 1.0 HE22 A:GLN242 4.9 41.3 1.0 H A:ALA238 4.9 37.7 1.0 HD13 A:LEU166 4.9 34.3 1.0 CA A:GLN242 4.9 33.2 1.0 CA A:ALA235 5.0 17.8 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:43.0 occ:1.00 F B:8WP403 0.0 43.0 1.0 C8 B:8WP403 1.3 40.0 1.0 F1 B:8WP403 2.1 52.0 1.0 F2 B:8WP403 2.1 43.6 1.0 C4 B:8WP403 2.3 39.6 1.0 HG2 B:GLN242 2.7 48.2 1.0 HB3 B:GLN242 2.9 38.6 1.0 N2 B:8WP403 3.0 46.8 1.0 HB B:ILE245 3.3 33.4 1.0 CG B:GLN242 3.3 40.1 1.0 HG21 B:ILE245 3.4 31.0 1.0 C5 B:8WP403 3.4 43.5 1.0 HG22 B:ILE245 3.4 31.0 1.0 HD12 B:ILE245 3.5 32.7 1.0 CB B:GLN242 3.5 32.1 1.0 HA B:GLN242 3.6 34.2 1.0 HO2 B:FMT402 3.6 74.3 1.0 CD B:GLN242 3.6 39.1 1.0 HG23 B:VAL246 3.7 28.4 1.0 CG2 B:ILE245 3.7 25.9 1.0 H5 B:8WP403 3.8 52.2 1.0 OE1 B:GLN242 3.8 29.6 1.0 CB B:ILE245 4.0 27.8 1.0 HD13 B:ILE245 4.0 32.7 1.0 CA B:GLN242 4.0 28.5 1.0 O B:GLN242 4.1 29.2 1.0 N1 B:8WP403 4.1 55.6 1.0 CD1 B:ILE245 4.1 27.2 1.0 HG3 B:GLN242 4.2 48.2 1.0 O2 B:FMT402 4.2 61.9 1.0 HB2 B:GLN242 4.3 38.6 1.0 NE2 B:GLN242 4.3 39.7 1.0 HB3 B:ALA217 4.3 30.6 1.0 C6 B:8WP403 4.4 53.4 1.0 HG22 B:VAL246 4.5 28.4 1.0 CG2 B:VAL246 4.5 23.7 1.0 C B:GLN242 4.5 35.0 1.0 HE21 B:GLN242 4.5 47.6 1.0 H B:VAL246 4.6 24.5 1.0 CG1 B:ILE245 4.7 37.2 1.0 HB3 B:LEU166 4.7 27.9 1.0 HG23 B:ILE245 4.7 31.0 1.0 HD13 B:LEU166 4.8 33.6 1.0 HG21 B:VAL246 4.8 28.4 1.0 HE22 B:GLN242 4.8 47.6 1.0 HG22 B:VAL237 4.8 43.1 1.0 C B:FMT402 4.9 63.3 1.0 HA B:VAL237 5.0 42.4 1.0 HB1 B:ALA235 5.0 33.3 1.0 HD11 B:ILE245 5.0 32.7 1.0 N B:VAL246 5.0 20.4 1.0 O B:ASP236 5.0 34.9 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:52.0 occ:1.00 F1 B:8WP403 0.0 52.0 1.0 C8 B:8WP403 1.3 40.0 1.0 F B:8WP403 2.1 43.0 1.0 F2 B:8WP403 2.1 43.6 1.0 C4 B:8WP403 2.3 39.6 1.0 HB3 B:LEU166 2.6 27.9 1.0 H5 B:8WP403 2.8 52.2 1.0 C5 B:8WP403 2.9 43.5 1.0 HD13 B:LEU166 3.1 33.6 1.0 HB2 B:LEU166 3.3 27.9 1.0 CB B:LEU166 3.4 23.2 1.0 HG22 B:ILE245 3.4 31.0 1.0 N2 B:8WP403 3.5 46.8 1.0 HG23 B:VAL246 3.5 28.4 1.0 HG22 B:VAL246 3.6 28.4 1.0 HD12 B:LEU166 3.7 33.6 1.0 HB3 B:ALA217 3.7 30.6 1.0 CD1 B:LEU166 3.7 28.0 1.0 HB1 B:ALA235 3.8 33.3 1.0 HG21 B:ILE245 3.9 31.0 1.0 CG2 B:VAL246 4.0 23.7 1.0 CG2 B:ILE245 4.1 25.9 1.0 CG B:LEU166 4.1 25.6 1.0 HB1 B:ALA217 4.1 30.6 1.0 C6 B:8WP403 4.2 53.4 1.0 CB B:ALA217 4.3 25.5 1.0 HB2 B:ALA235 4.3 33.3 1.0 HB B:ILE245 4.3 33.4 1.0 HD22 B:LEU166 4.3 36.5 1.0 C B:LEU166 4.4 25.1 1.0 N1 B:8WP403 4.4 55.6 1.0 HB3 B:GLN242 4.4 38.6 1.0 HB2 B:ALA217 4.4 30.6 1.0 CA B:LEU166 4.5 36.5 1.0 CB B:ALA235 4.5 27.7 1.0 HG21 B:VAL246 4.5 28.4 1.0 HD11 B:LEU166 4.6 33.6 1.0 O B:LEU166 4.6 25.6 1.0 HA B:VAL246 4.6 33.1 1.0 N B:GLY167 4.7 28.0 1.0 HG2 B:GLN242 4.8 48.2 1.0 HA B:LEU166 4.8 43.8 1.0 CB B:ILE245 4.8 27.8 1.0 H B:GLY167 4.8 33.6 1.0 H B:VAL246 4.8 24.5 1.0 CD2 B:LEU166 4.8 30.4 1.0 HG23 B:ILE245 4.8 31.0 1.0 N B:VAL246 4.9 20.4 1.0 HA3 B:GLY167 4.9 33.6 1.0 HG B:LEU166 4.9 30.7 1.0 O B:GLN242 5.0 29.2 1.0 HO2 B:FMT402 5.0 74.3 1.0

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


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 1A within 5.0Å range: probe atom residue distance (Å) B Occ B:F403 b:43.6 occ:1.00 F2 B:8WP403 0.0 43.6 1.0 C8 B:8WP403 1.3 40.0 1.0 F1 B:8WP403 2.1 52.0 1.0 F B:8WP403 2.1 43.0 1.0 C4 B:8WP403 2.3 39.6 1.0 N2 B:8WP403 2.8 46.8 1.0 O B:ASP236 3.1 34.9 1.0 HB1 B:ALA235 3.2 33.3 1.0 HB3 B:GLN242 3.2 38.6 1.0 OE1 B:GLN242 3.5 29.6 1.0 C5 B:8WP403 3.5 43.5 1.0 HG23 B:VAL246 3.8 28.4 1.0 HA B:VAL237 3.8 42.4 1.0 HG22 B:VAL246 3.9 28.4 1.0 CD B:GLN242 4.0 39.1 1.0 HG22 B:VAL237 4.0 43.1 1.0 N1 B:8WP403 4.0 55.6 1.0 H5 B:8WP403 4.0 52.2 1.0 C B:ASP236 4.0 34.6 1.0 HG2 B:GLN242 4.0 48.2 1.0 CB B:GLN242 4.1 32.1 1.0 CB B:ALA235 4.1 27.7 1.0 HB3 B:LEU166 4.1 27.9 1.0 CG2 B:VAL246 4.1 23.7 1.0 H B:ASP236 4.2 31.4 1.0 HG21 B:VAL246 4.2 28.4 1.0 HB2 B:LEU166 4.2 27.9 1.0 CG B:GLN242 4.3 40.1 1.0 C6 B:8WP403 4.4 53.4 1.0 HB2 B:ALA235 4.4 33.3 1.0 N B:ASP236 4.6 26.2 1.0 HB3 B:ALA235 4.6 33.3 1.0 HB2 B:GLN242 4.6 38.6 1.0 CA B:VAL237 4.6 35.4 1.0 O B:LEU166 4.6 25.6 1.0 HG23 B:VAL237 4.7 43.1 1.0 HA3 B:GLY167 4.7 33.6 1.0 CB B:LEU166 4.7 23.2 1.0 N B:VAL237 4.7 31.9 1.0 CG2 B:VAL237 4.7 36.0 1.0 O B:GLN242 4.7 29.2 1.0 O B:HOH503 4.8 29.8 1.0 NE2 B:GLN242 4.9 39.7 1.0 HD13 B:LEU166 4.9 33.6 1.0 HA B:ALA235 4.9 28.0 1.0 C B:LEU166 4.9 25.1 1.0 HG22 B:ILE245 5.0 31.0 1.0 HA B:GLN242 5.0 34.2 1.0 H B:ALA238 5.0 41.5 1.0 CA B:ASP236 5.0 26.6 1.0 HB B:ILE245 5.0 33.4 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