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Fluorine in PDB 8g9d: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7:
3.6.1.52;

Protein crystallography data

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7, PDB code: 8g9d was solved by G.Zong, H.Wang, S.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.63 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.444, 59.711, 62.402, 90, 90, 90
R / Rfree (%) 19.1 / 22.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7 (pdb code 8g9d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7, PDB code: 8g9d:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 8g9d

Go back to Fluorine Binding Sites List in 8g9d
Fluorine binding site 1 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.8
occ:1.00
 F55 A:KDJ401 0.0 39.8 1.0
C45 A:KDJ401 1.3 37.1 1.0
F65 A:KDJ401 2.2 35.6 1.0
C25 A:KDJ401 2.3 31.6 1.0
PB5 A:KDJ401 2.6 43.5 1.0
O35 A:KDJ401 2.7 31.1 1.0
O95 A:KDJ401 2.9 49.5 1.0
O85 A:KDJ401 3.0 43.7 1.0
NH2 A:ARG89 3.3 36.7 1.0
CZ A:ARG89 3.3 35.8 1.0
N15 A:KDJ401 3.6 24.9 1.0
NH1 A:ARG89 3.7 38.5 1.0
NE A:ARG89 3.8 31.2 1.0
O75 A:KDJ401 3.9 37.5 1.0
O46 A:KDJ401 4.4 25.8 1.0
CD A:ARG89 4.5 26.8 1.0
NE A:ARG41 4.6 51.8 1.0
C5 A:KDJ401 4.7 23.3 1.0
O16 A:KDJ401 4.7 23.5 1.0
NH2 A:ARG41 4.9 55.3 1.0
O36 A:KDJ401 4.9 30.4 1.0
PA6 A:KDJ401 5.0 27.6 1.0

Fluorine binding site 2 out of 2 in 8g9d

Go back to Fluorine Binding Sites List in 8g9d
Fluorine binding site 2 out of 2 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Phosphonodifluoroacetamide Inositol Pentakisphosphate (5-PCF2AM-INSP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.6
occ:1.00
 F65 A:KDJ401 0.0 35.6 1.0
C45 A:KDJ401 1.3 37.1 1.0
F55 A:KDJ401 2.2 39.8 1.0
C25 A:KDJ401 2.3 31.6 1.0
PB5 A:KDJ401 2.6 43.5 1.0
N15 A:KDJ401 2.7 24.9 1.0
O75 A:KDJ401 3.0 37.5 1.0
O95 A:KDJ401 3.0 49.5 1.0
NE A:ARG89 3.0 31.2 1.0
O46 A:KDJ401 3.1 25.8 1.0
O A:HOH505 3.4 27.6 1.0
CD A:ARG89 3.4 26.8 1.0
CZ A:ARG89 3.4 35.8 1.0
O35 A:KDJ401 3.5 31.1 1.0
NH2 A:ARG89 3.8 36.7 1.0
CG A:ARG89 3.9 22.4 1.0
O85 A:KDJ401 3.9 43.7 1.0
NH1 A:ARG89 4.0 38.5 1.0
C5 A:KDJ401 4.1 23.3 1.0
PA6 A:KDJ401 4.3 27.6 1.0
O16 A:KDJ401 4.4 23.5 1.0
NZ A:LYS133 4.6 24.6 1.0
C6 A:KDJ401 4.7 23.7 1.0
O36 A:KDJ401 4.7 30.4 1.0
CB A:ARG89 4.9 19.0 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: Fri Aug 2 19:41:22 2024

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