Fluorine in PDB 8gzc: Crystal Structure of EP300 Hat Domain in Complex with Compound 10

All present enzymatic activity of Crystal Structure of EP300 Hat Domain in Complex with Compound 10:
2.3.1.48;

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 10, PDB code: 8gzc was solved by M.Takahashi, H.Hanzawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.00
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.5, 89.35, 91.6, 116.6, 95.18, 91.78
R / Rfree (%)	19.5 / 22.7

The structure of Crystal Structure of EP300 Hat Domain in Complex with Compound 10 also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Fluorine atom in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10 (pdb code 8gzc). 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 EP300 Hat Domain in Complex with Compound 10, PDB code: 8gzc:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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 EP300 Hat Domain in Complex with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1704 b:50.5 occ:1.00 FBG A:KQO1704 0.0 50.5 1.0 CG A:KQO1704 1.3 45.9 1.0 CB A:KQO1704 2.2 41.4 1.0 CD A:KQO1704 2.2 38.6 1.0 CA A:KQO1704 2.8 37.7 1.0 O A:KQO1704 2.8 40.0 1.0 C A:KQO1704 2.8 44.2 1.0 N A:KQO1704 2.9 43.6 1.0 CG A:PRO1458 3.3 42.4 1.0 CD A:PRO1458 3.3 39.3 1.0 CD A:PRO1440 3.4 47.4 1.0 NAV A:KQO1704 3.7 44.0 1.0 CA A:PRO1439 4.1 50.0 1.0 CAO A:KQO1704 4.2 41.5 1.0 CD2 A:LEU1463 4.3 34.5 1.0 CG A:PRO1440 4.3 42.9 1.0 CB A:PRO1439 4.4 50.0 1.0 CG2 A:ILE1457 4.4 41.8 1.0 CAW A:KQO1704 4.5 50.6 1.0 N A:PRO1458 4.5 43.5 1.0 N A:PRO1440 4.5 56.3 1.0 CD1 A:LEU1463 4.7 38.3 1.0 CB A:PRO1458 4.8 38.9 1.0 C A:PRO1439 4.9 55.9 1.0 OBH A:KQO1704 4.9 37.8 1.0 CAC A:KQO1704 5.0 46.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of EP300 Hat Domain in Complex with Compound 10


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 EP300 Hat Domain in Complex with Compound 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1704 b:58.4 occ:1.00 FBG B:KQO1704 0.0 58.4 1.0 CG B:KQO1704 1.3 49.2 1.0 CD B:KQO1704 2.2 46.8 1.0 CB B:KQO1704 2.2 40.1 1.0 O B:KQO1704 2.8 49.7 1.0 CA B:KQO1704 2.8 45.7 1.0 C B:KQO1704 2.8 52.1 1.0 N B:KQO1704 2.9 43.1 1.0 CD B:PRO1440 3.3 47.1 1.0 CD B:PRO1458 3.4 48.9 1.0 CG B:PRO1458 3.4 57.8 1.0 NAV B:KQO1704 3.7 53.8 1.0 CA B:PRO1439 4.0 62.6 1.0 CAO B:KQO1704 4.2 53.5 1.0 CG B:PRO1440 4.3 55.4 1.0 CB B:PRO1439 4.3 56.4 1.0 CD2 B:LEU1463 4.4 45.6 1.0 CAW B:KQO1704 4.4 57.0 1.0 N B:PRO1440 4.5 56.6 1.0 CG2 B:ILE1457 4.5 59.4 1.0 N B:PRO1458 4.6 52.1 1.0 CD1 B:LEU1463 4.7 44.4 1.0 C B:PRO1439 4.8 58.0 1.0 CB B:PRO1458 4.9 52.2 1.0 OBH B:KQO1704 4.9 43.8 1.0 O B:CYS1438 4.9 63.6 1.0 N B:PRO1439 5.0 58.6 1.0 CAC B:KQO1704 5.0 48.3 1.0

R.Kanada, Y.Kagoshima, T.Suzuki, A.Nakamura, H.Funami, J.Watanabe, M.Asano, M.Takahashi, O.Ubukata, K.Suzuki, T.Aikawa, K.Sato, M.Goto, G.Setsu, K.Ito, K.Kihara, M.Kuroha, T.Kohno, H.Ogiwara, T.Isoyama, Y.Tominaga, S.Higuchi, H.Naito. Discovery of Ds-9300: A Highly Potent, Selective, and Once-Daily Oral EP300/Cbp Histone Acetyltransferase Inhibitor. J.Med.Chem. 2022.
ISSN: ISSN 0022-2623
PubMed: 36572866
DOI: 10.1021/ACS.JMEDCHEM.2C01641