Fluorine in PDB 8k5y: 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: 8k5y 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)	49.01 / 1.52
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.53, 73.99, 77.13, 90, 103.36, 90
R / Rfree (%)	17.6 / 19.8

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 8k5y). 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: 8k5y:
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:30.8 occ:1.00 FAY A:VP6306 0.0 30.8 1.0 CAT A:VP6306 1.4 30.0 1.0 CAR A:VP6306 2.4 27.4 1.0 CAU A:VP6306 2.5 28.2 1.0 CAS A:VP6306 2.7 29.2 1.0 NAX A:VP6306 2.7 29.7 1.0 O A:ARG106 2.9 37.4 1.0 N A:GLN108 3.1 36.4 1.0 OAL A:VP6306 3.2 30.1 1.0 CE1 A:TYR179 3.6 27.1 1.0 NAV A:VP6306 3.7 27.4 1.0 CAQ A:VP6306 3.7 30.2 1.0 OH A:TYR179 3.7 34.1 1.0 CB A:GLN108 3.7 36.8 1.0 C A:PHE107 3.7 43.6 1.0 NAM A:VP6306 3.8 28.9 1.0 CA A:PHE107 3.8 41.4 1.0 CZ A:TYR179 3.9 27.8 1.0 CA A:GLN108 3.9 33.5 1.0 CAK A:VP6306 3.9 29.9 1.0 C A:ARG106 4.0 43.2 1.0 CAW A:VP6306 4.2 26.9 1.0 CD1 A:TYR179 4.4 25.0 1.0 N A:PHE107 4.4 45.3 1.0 CG A:PRO102 4.7 20.7 1.0 O A:PHE107 4.8 42.5 1.0 CE2 A:TYR179 4.9 26.6 1.0 CAP A:VP6306 4.9 29.9 1.0 CG A:GLN108 5.0 36.8 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:24.6 occ:1.00 FAY B:VP6306 0.0 24.6 1.0 CAT B:VP6306 1.4 22.5 1.0 CAU B:VP6306 2.4 23.7 1.0 CAR B:VP6306 2.4 21.9 1.0 NAX B:VP6306 2.7 27.4 1.0 CAS B:VP6306 2.8 23.8 1.0 O B:ARG106 2.8 28.9 1.0 N B:GLN108 3.3 25.9 1.0 OAL B:VP6306 3.3 21.1 1.0 CE1 B:TYR179 3.5 21.9 1.0 NAV B:VP6306 3.6 24.2 1.0 CAQ B:VP6306 3.7 22.8 1.0 CA B:PHE107 3.7 23.6 1.0 C B:PHE107 3.7 28.1 1.0 OH B:TYR179 3.7 25.1 1.0 CZ B:TYR179 3.8 21.2 1.0 C B:ARG106 3.9 26.6 1.0 NAM B:VP6306 3.9 21.0 1.0 CAK B:VP6306 4.1 20.3 1.0 CAW B:VP6306 4.1 25.0 1.0 CB B:GLN108 4.1 27.1 1.0 N B:PHE107 4.3 27.3 1.0 CA B:GLN108 4.3 25.7 1.0 CD1 B:TYR179 4.4 20.4 1.0 O B:PHE107 4.6 29.0 1.0 CG B:PRO102 4.7 22.4 1.0 CE2 B:TYR179 4.8 21.0 1.0 CAP B:VP6306 4.9 23.3 1.0 CB B:PHE107 5.0 26.8 1.0 CD B:PRO102 5.0 18.8 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