Fluorine in PDB 7yi7: Crystal Structure of Human HPSE1 in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human HPSE1 in Complex with Inhibitor:
3.2.1.166;

The structure of Crystal Structure of Human HPSE1 in Complex with Inhibitor, PDB code: 7yi7 was solved by M.Mima, N.Fujimoto, Y.Imai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.73 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.974, 60.09, 78.423, 90, 89.16, 90
R / Rfree (%)	21.3 / 28.1

The binding sites of Fluorine atom in the Crystal Structure of Human HPSE1 in Complex with Inhibitor (pdb code 7yi7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human HPSE1 in Complex with Inhibitor, PDB code: 7yi7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human HPSE1 in Complex with Inhibitor


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 HPSE1 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:105.9 occ:1.00 F19 A:IUV601 0.0 105.9 1.0 C18 A:IUV601 1.3 112.8 1.0 F21 A:IUV601 2.1 104.1 1.0 F20 A:IUV601 2.2 124.8 1.0 C15 A:IUV601 2.3 111.2 1.0 C14 A:IUV601 2.7 107.5 1.0 CD1 A:TYR348 3.3 63.9 1.0 C16 A:IUV601 3.5 107.5 1.0 CE1 A:TYR348 3.6 66.2 1.0 C13 A:IUV601 4.0 105.5 1.0 CA A:GLY349 4.1 46.0 1.0 N A:GLY349 4.1 47.7 1.0 CG A:TYR348 4.5 58.9 1.0 C17 A:IUV601 4.7 102.5 1.0 O26 A:IUV601 4.7 41.5 1.0 NH1 A:ARG303 4.8 111.7 1.0 C12 A:IUV601 4.9 95.1 1.0 C A:TYR348 4.9 49.5 1.0 CB A:TYR348 4.9 54.7 1.0 CZ A:TYR348 4.9 68.9 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human HPSE1 in Complex with Inhibitor


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 HPSE1 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:104.1 occ:1.00 F21 A:IUV601 0.0 104.1 1.0 C18 A:IUV601 1.3 112.8 1.0 F19 A:IUV601 2.1 105.9 1.0 F20 A:IUV601 2.2 124.8 1.0 C15 A:IUV601 2.3 111.2 1.0 C16 A:IUV601 2.8 107.5 1.0 C14 A:IUV601 3.6 107.5 1.0 O26 A:IUV601 4.1 41.5 1.0 C17 A:IUV601 4.1 102.5 1.0 CA A:GLY349 4.4 46.0 1.0 N A:GLY349 4.6 47.7 1.0 C13 A:IUV601 4.7 105.5 1.0 C12 A:IUV601 4.9 95.1 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human HPSE1 in Complex with Inhibitor


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 HPSE1 in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:124.8 occ:1.00 F20 A:IUV601 0.0 124.8 1.0 C18 A:IUV601 1.3 112.8 1.0 F19 A:IUV601 2.2 105.9 1.0 F21 A:IUV601 2.2 104.1 1.0 C15 A:IUV601 2.3 111.2 1.0 C14 A:IUV601 3.1 107.5 1.0 C16 A:IUV601 3.1 107.5 1.0 C13 A:IUV601 4.4 105.5 1.0 C17 A:IUV601 4.4 102.5 1.0 C12 A:IUV601 4.9 95.1 1.0

Y.Imai, D.Wakasugi, R.Suzuki, S.Kato, M.Sugisaki, M.Mima, H.Miyagawa, M.Endo, N.Fujimoto, T.Fukunaga, S.Kato, S.Kuroda, T.Takahashi, H.Kakinuma. Lead Identification of Novel Tetrahydroimidazo[1,2-A]Pyridine-5-Carboxylic Acid Derivative As A Potent Heparanase-1 Inhibitor. Bioorg.Med.Chem.Lett. V. 79 29050 2022.
ISSN: ESSN 1464-3405
PubMed: 36368497
DOI: 10.1016/J.BMCL.2022.129050