Fluorine in PDB 7zi3: Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor

All present enzymatic activity of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor:
2.7.1.113; 2.7.1.74; 2.7.1.76;

The structure of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor, PDB code: 7zi3 was solved by K.Ben-Yaala, M.Saez-Ayala, S.Betzi, E.Rebuffet, X.Morelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 1.90
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.94, 68.94, 120.763, 90, 90, 90
R / Rfree (%)	19 / 23

The structure of Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor (pdb code 7zi3). 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 Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor, PDB code: 7zi3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 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 Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:64.5 occ:1.00 F1 A:J98301 0.0 64.5 1.0 C25 A:J98301 1.3 60.8 1.0 F2 A:J98301 2.1 60.6 1.0 F3 A:J98301 2.2 59.7 1.0 C24 A:J98301 2.3 58.9 1.0 C23 A:J98301 2.7 55.8 1.0 CD A:PRO201 3.2 56.4 1.0 C14 A:J98301 3.6 50.2 1.0 CA A:ILE200 3.9 57.6 1.0 CG1 A:ILE200 4.0 59.0 1.0 C17 A:J98301 4.1 51.2 1.0 CG A:PRO201 4.1 62.6 1.0 C13 A:J98301 4.3 46.0 1.0 CD2 A:TYR204 4.3 46.2 1.0 CB A:ILE200 4.3 54.9 1.0 N A:PRO201 4.3 56.0 1.0 CB A:TYR204 4.4 51.2 1.0 CG A:TYR204 4.4 47.1 1.0 CG2 A:ILE200 4.5 56.2 1.0 C A:ILE200 4.7 56.0 1.0 C15 A:J98301 4.8 50.6 1.0 O2 A:J98301 4.8 63.6 1.0 C26 A:J98301 4.8 47.3 1.0 N A:ILE200 4.8 60.3 1.0 C12 A:J98301 4.9 47.9 1.0 C16 A:J98301 4.9 57.1 1.0 O A:GLY199 4.9 60.6 1.0 CE2 A:TYR204 4.9 49.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 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 Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:60.6 occ:1.00 F2 A:J98301 0.0 60.6 1.0 C25 A:J98301 1.3 60.8 1.0 F3 A:J98301 2.1 59.7 1.0 F1 A:J98301 2.1 64.5 1.0 C24 A:J98301 2.3 58.9 1.0 C13 A:J98301 2.9 46.0 1.0 C14 A:J98301 3.0 50.2 1.0 C12 A:J98301 3.1 47.9 1.0 CG1 A:ILE200 3.4 59.0 1.0 C23 A:J98301 3.4 55.8 1.0 C26 A:J98301 3.6 47.3 1.0 CD2 A:TYR204 3.8 46.2 1.0 CE2 A:TYR204 3.8 49.2 1.0 C11 A:J98301 4.0 46.5 1.0 CD1 A:ILE200 4.1 62.3 1.0 C15 A:J98301 4.3 50.6 1.0 C27 A:J98301 4.3 46.5 1.0 CB A:ILE200 4.4 54.9 1.0 CG A:TYR204 4.5 47.1 1.0 C28 A:J98301 4.5 49.5 1.0 CG2 A:ILE200 4.6 56.2 1.0 CZ A:TYR204 4.6 47.8 1.0 C17 A:J98301 4.6 51.2 1.0 CA A:ILE200 4.6 57.6 1.0 CE1 A:TYR86 4.7 51.7 1.0 C2 A:J98301 4.7 52.1 1.0 N1 A:J98301 4.8 48.6 1.0 CD A:PRO201 4.9 56.4 1.0 C16 A:J98301 4.9 57.1 1.0 C3 A:J98301 5.0 50.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Dck C4S-S74E Mutant in Complex with Udp and the OR0642 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 Dck C4S-S74E Mutant in Complex with Udp and the OR0642 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:59.7 occ:1.00 F3 A:J98301 0.0 59.7 1.0 C25 A:J98301 1.3 60.8 1.0 F2 A:J98301 2.1 60.6 1.0 F1 A:J98301 2.2 64.5 1.0 C24 A:J98301 2.4 58.9 1.0 C14 A:J98301 3.0 50.2 1.0 C26 A:J98301 3.0 47.3 1.0 C13 A:J98301 3.0 46.0 1.0 C23 A:J98301 3.4 55.8 1.0 C27 A:J98301 4.0 46.5 1.0 C12 A:J98301 4.0 47.9 1.0 C15 A:J98301 4.3 50.6 1.0 C17 A:J98301 4.6 51.2 1.0 CE1 A:TYR86 4.7 51.7 1.0 C11 A:J98301 4.7 46.5 1.0 C28 A:J98301 4.7 49.5 1.0 CD1 A:TYR86 4.8 54.9 1.0 CG1 A:ILE200 4.8 59.0 1.0 C16 A:J98301 5.0 57.1 1.0

M.Saez-Ayala, L.Hoffer, S.Abel, K.Ben Yaala, B.Sicard, G.P.Andrieu, M.Latiri, E.K.Davison, M.A.Ciufolini, P.Bremond, E.Rebuffet, P.Roche, C.Derviaux, E.Voisset, C.Montersino, R.Castellano, Y.Collette, V.Asnafi, S.Betzi, P.Dubreuil, S.Combes, X.Morelli. From A Drug Repositioning to A Structure-Based Drug Design Approach to Tackle Acute Lymphoblastic Leukemia. Nat Commun V. 14 3079 2023.
ISSN: ESSN 2041-1723
PubMed: 37248212
DOI: 10.1038/S41467-023-38668-2