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Fluorine in PDB 8g9e: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7:
2.7.4.21; 2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7, PDB code: 8g9e was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.52 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.082, 109.899, 41.09, 90, 90, 90
R / Rfree (%) 12.4 / 17.5

Other elements in 8g9e:

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 (pdb code 8g9e). 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 Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7, PDB code: 8g9e:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8g9e

Go back to Fluorine Binding Sites List in 8g9e
Fluorine binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7


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 Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:32.6
occ:1.00
 F51 A:YUT402 0.0 32.6 1.0
C45 A:YUT402 1.3 28.4 1.0
F52 A:YUT402 2.2 31.6 1.0
PA5 A:YUT402 2.5 24.9 1.0
O26 A:YUT402 2.6 31.6 1.0
PB5 A:YUT402 2.8 32.4 1.0
O65 A:YUT402 2.9 38.0 1.0
NZ A:LYS214 2.9 25.5 1.0
O25 A:YUT402 2.9 22.1 1.0
O15 A:YUT402 3.0 23.6 1.0
O36 A:YUT402 3.1 30.2 1.0
O55 A:YUT402 3.2 33.5 1.0
PA6 A:YUT402 3.2 27.6 1.0
O A:HOH611 3.2 36.5 1.0
O16 A:YUT402 3.4 24.0 1.0
CE A:LYS214 3.4 28.0 1.0
NZ A:LYS278 3.6 78.7 1.0
O A:HOH507 3.7 44.2 1.0
O35 A:YUT402 3.8 28.2 1.0
O75 A:YUT402 3.9 37.7 1.0
C5 A:YUT402 4.0 20.0 1.0
C6 A:YUT402 4.2 22.1 1.0
O A:HOH619 4.3 35.5 1.0
O46 A:YUT402 4.7 30.1 1.0
CD A:LYS214 4.7 28.6 1.0
NH1 A:ARG273 4.8 30.7 1.0
O A:HOH533 5.0 28.5 1.0

Fluorine binding site 2 out of 2 in 8g9e

Go back to Fluorine Binding Sites List in 8g9e
Fluorine binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7


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 Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Amp-Pnp and 5- (PCF2P)-IP5, An Analog of 5-IP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:31.6
occ:1.00
 F52 A:YUT402 0.0 31.6 1.0
C45 A:YUT402 1.4 28.4 1.0
F51 A:YUT402 2.2 32.6 1.0
PA5 A:YUT402 2.7 24.9 1.0
PB5 A:YUT402 2.8 32.4 1.0
O15 A:YUT402 2.9 23.6 1.0
O75 A:YUT402 3.0 37.7 1.0
O A:HOH533 3.1 28.5 1.0
O A:HOH619 3.1 35.5 1.0
O65 A:YUT402 3.1 38.0 1.0
O35 A:YUT402 3.1 28.2 1.0
O A:HOH774 3.4 43.8 1.0
NZ A:LYS278 3.4 78.7 1.0
O36 A:YUT402 3.6 30.2 1.0
O A:HOH507 3.6 44.2 1.0
O A:HOH502 3.8 22.9 1.0
O25 A:YUT402 4.0 22.1 1.0
O55 A:YUT402 4.0 33.5 1.0
C5 A:YUT402 4.3 20.0 1.0
PA6 A:YUT402 4.4 27.6 1.0
O26 A:YUT402 4.5 31.6 1.0
O16 A:YUT402 4.5 24.0 1.0
C6 A:YUT402 4.7 22.1 1.0
O A:HOH611 4.7 36.5 1.0
CE A:LYS278 4.8 76.0 1.0
O A:HOH618 4.9 34.4 1.0

Reference:

S.Hostachy, H.Wang, G.Zong, K.Franke, A.M.Riley, P.Schmieder, B.V.L.Potter, S.B.Shears, D.Fiedler. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry V. 29 02426 2023.
ISSN: ISSN 0947-6539
PubMed: 37773020
DOI: 10.1002/CHEM.202302426
Page generated: Wed Jul 16 04:57:14 2025

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