Fluorine in PDB 8k5w: Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor:
3.4.24.35;

The structure of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor, PDB code: 8k5w was solved by M.Kamitani, M.Mima, R.Nishikawa-Shimono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.57 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.319, 73.002, 75.994, 90, 102.57, 90
R / Rfree (%)	22.5 / 27.3

The structure of Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor also contains other interesting chemical elements:

Zinc	(Zn)	4 atoms
Calcium	(Ca)	6 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor (pdb code 8k5w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Prommp-9 Catalytic Domain in Complex with Inhibitor, PDB code: 8k5w:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Prommp-9 Catalytic Domain 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 Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F306 b:54.7 occ:1.00 F3 A:VOO306 0.0 54.7 1.0 C2 A:VOO306 1.3 50.5 1.0 C4 A:VOO306 2.4 49.9 1.0 C1 A:VOO306 2.4 48.6 1.0 C5 A:VOO306 3.6 42.0 1.0 C32 A:VOO306 3.7 42.8 1.0 CG A:PRO102 3.9 29.7 1.0 OH A:TYR179 4.1 61.2 1.0 CE1 A:TYR179 4.1 47.6 1.0 C31 A:VOO306 4.2 47.7 1.0 CD A:PRO102 4.3 31.6 1.0 CZ A:TYR179 4.4 53.5 1.0 O A:GLY105 4.4 51.8 1.0 N33 A:VOO306 4.8 42.4 1.0 C6 A:VOO306 4.9 46.7 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Prommp-9 Catalytic Domain 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 Prommp-9 Catalytic Domain in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F306 b:64.9 occ:1.00 F3 B:VOO306 0.0 64.9 1.0 C2 B:VOO306 1.4 55.0 1.0 C4 B:VOO306 2.4 52.7 1.0 C1 B:VOO306 2.4 49.6 1.0 C5 B:VOO306 3.6 48.7 1.0 OH B:TYR179 3.6 79.6 1.0 C32 B:VOO306 3.7 47.3 1.0 CG B:PRO102 3.7 50.6 1.0 CE1 B:TYR179 3.8 68.6 1.0 CZ B:TYR179 4.1 71.2 1.0 C31 B:VOO306 4.1 47.4 1.0 CD B:PRO102 4.2 48.0 1.0 N33 B:VOO306 4.9 43.8 1.0 C6 B:VOO306 4.9 46.0 1.0 CD1 B:TYR179 4.9 64.9 1.0 CZ B:PHE110 5.0 43.1 1.0 CE2 B:PHE110 5.0 43.0 1.0

R.Nishikawa-Shimono, M.Kuwabara, S.Fujisaki, D.Matsuda, M.Endo, M.Kamitani, A.Futamura, Y.Nomura, T.Yamaguchi-Sasaki, T.Yabuuchi, C.Yamaguchi, N.Tanaka-Yamamoto, S.Satake, K.Abe-Sato, K.Funayama, M.Sakata, S.Takahashi, K.Hirano, T.Fukunaga, Y.Uozumi, S.Kato, Y.Tamura, T.Nakamori, M.Mima, C.Mishima-Tsumagari, D.Nozawa, Y.Imai, T.Asami. Discovery of Novel Indole Derivatives As Potent and Selective Inhibitors of Prommp-9 Activation. Bioorg.Med.Chem.Lett. V. 97 29541 2023.
ISSN: ESSN 1464-3405
PubMed: 37952596
DOI: 10.1016/J.BMCL.2023.129541