Fluorine in PDB 6n5c: Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5:
2.7.4.21; 2.7.4.24;

The structure of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5, PDB code: 6n5c was solved by H.Wang, S.B.Shears, A.Riley, B.Potter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.17 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.604, 111.032, 41.429, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 21.4

The structure of Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5 (pdb code 6n5c). 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 the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5, PDB code: 6n5c:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5


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 the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F406 b:59.5 occ:1.00 F55 A:KDJ406 0.0 59.5 1.0 C45 A:KDJ406 1.3 59.9 1.0 F65 A:KDJ406 2.2 60.5 1.0 C25 A:KDJ406 2.4 54.1 1.0 N15 A:KDJ406 2.5 47.8 1.0 PB5 A:KDJ406 2.7 66.6 1.0 O95 A:KDJ406 2.8 69.0 1.0 O A:HOH657 3.0 53.0 1.0 O85 A:KDJ406 3.0 60.5 1.0 O A:HOH668 3.2 55.3 1.0 O35 A:KDJ406 3.5 48.6 1.0 O34 A:KDJ406 3.6 52.4 1.0 O75 A:KDJ406 3.8 66.6 1.0 C5 A:KDJ406 4.0 45.5 1.0 O36 A:KDJ406 4.3 45.0 1.0 O14 A:KDJ406 4.5 47.8 1.0 C4 A:KDJ406 4.6 44.1 1.0 PA4 A:KDJ406 4.8 53.1 1.0 C6 A:KDJ406 4.8 45.9 1.0 O A:HOH553 4.9 65.2 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5


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 the Catalytic Domain of PPIP5K2 in Complex with Amppnp and 5-PCF2AM-INSP5 within 5.0Å range: probe atom residue distance (Å) B Occ A:F406 b:60.5 occ:1.00 F65 A:KDJ406 0.0 60.5 1.0 C45 A:KDJ406 1.4 59.9 1.0 F55 A:KDJ406 2.2 59.5 1.0 C25 A:KDJ406 2.4 54.1 1.0 O A:HOH668 2.4 55.3 1.0 PB5 A:KDJ406 2.7 66.6 1.0 O35 A:KDJ406 2.8 48.6 1.0 O75 A:KDJ406 2.9 66.6 1.0 O95 A:KDJ406 2.9 69.0 1.0 N15 A:KDJ406 3.4 47.8 1.0 O85 A:KDJ406 3.8 60.5 1.0 O A:HOH553 4.0 65.2 1.0 NZ A:LYS214 4.2 55.0 1.0 O34 A:KDJ406 4.2 52.4 1.0 C5 A:KDJ406 4.6 45.5 1.0 O14 A:KDJ406 4.8 47.8 1.0 O A:HOH657 5.0 53.0 1.0

A.M.Riley, H.Wang, S.B.Shears, B.V.L.Potter. Synthesis of An Alpha-Phosphono-Alpha , Alpha-Difluoroacetamide Analogue of the Diphosphoinositol Pentakisphosphate 5-INSP7. Medchemcomm V. 10 1165 2019.
ISSN: ESSN 2040-2511
PubMed: 31391889
DOI: 10.1039/C9MD00163H