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Fluorine in PDB 8g9c: Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7

Enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7

All present enzymatic activity of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), 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- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7, PDB code: 8g9c 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) 31.72 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.752, 59.639, 62.409, 90, 90, 90
R / Rfree (%) 17 / 18.8

Other elements in 8g9c:

The structure of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 (pdb code 8g9c). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7, PDB code: 8g9c:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8g9c

Go back to Fluorine Binding Sites List in 8g9c
Fluorine binding site 1 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), 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- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:41.4
occ:1.00
 F51 A:YUT401 0.0 41.4 1.0
C45 A:YUT401 1.3 51.5 1.0
F52 A:YUT401 2.2 56.8 1.0
PA5 A:YUT401 2.6 58.0 1.0
PB5 A:YUT401 2.6 51.3 1.0
O15 A:YUT401 2.7 37.7 1.0
O36 A:YUT401 2.8 33.7 1.0
O65 A:YUT401 3.0 42.7 1.0
O A:HOH504 3.0 32.6 1.0
O75 A:YUT401 3.0 58.1 1.0
NE A:ARG89 3.3 33.6 1.0
O25 A:YUT401 3.5 56.5 1.0
CD A:ARG89 3.7 28.5 1.0
O35 A:YUT401 3.8 62.0 1.0
CZ A:ARG89 3.9 40.5 1.0
O55 A:YUT401 3.9 52.9 1.0
CG A:ARG89 3.9 26.8 1.0
C5 A:YUT401 4.1 27.2 1.0
NH2 A:ARG89 4.1 40.5 1.0
PA6 A:YUT401 4.2 32.5 1.0
O16 A:YUT401 4.6 29.4 1.0
C6 A:YUT401 4.7 26.0 1.0
O A:HOH590 4.7 38.0 1.0
NH1 A:ARG89 4.7 42.0 1.0
O26 A:YUT401 4.8 39.5 1.0
C4 A:YUT401 4.8 22.0 1.0
CB A:ARG89 4.9 21.6 1.0
O14 A:YUT401 4.9 25.3 1.0

Fluorine binding site 2 out of 3 in 8g9c

Go back to Fluorine Binding Sites List in 8g9c
Fluorine binding site 2 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), 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- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:56.8
occ:1.00
 F52 A:YUT401 0.0 56.8 1.0
C45 A:YUT401 1.3 51.5 1.0
F51 A:YUT401 2.2 41.4 1.0
PA5 A:YUT401 2.6 58.0 1.0
PB5 A:YUT401 2.6 51.3 1.0
O25 A:YUT401 2.8 56.5 1.0
O75 A:YUT401 2.9 58.1 1.0
O55 A:YUT401 3.1 52.9 1.0
CZ A:ARG89 3.1 40.5 1.0
NH2 A:ARG89 3.2 40.5 1.0
NE A:ARG89 3.3 33.6 1.0
O35 A:YUT401 3.6 62.0 1.0
NH1 A:ARG89 3.7 42.0 1.0
O15 A:YUT401 3.7 37.7 1.0
O65 A:YUT401 3.9 42.7 1.0
O36 A:YUT401 3.9 33.7 1.0
CD A:ARG89 4.1 28.5 1.0
O26 A:YUT401 4.8 39.5 1.0
PA6 A:YUT401 4.9 32.5 1.0
CG A:ARG89 5.0 26.8 1.0

Fluorine binding site 3 out of 3 in 8g9c

Go back to Fluorine Binding Sites List in 8g9c
Fluorine binding site 3 out of 3 in the Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), 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 3 of Diphosphoinositol Polyphosphate Phosphohydrolase 1 (DIPP1/NUDT3) in Complex with 5- Difluoromethylenebisphosphonate Inositol Pentakisphosphate (5-PCF2P-IP5), An Analogue of 5-INSP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F408

b:34.1
occ:1.00
 MG A:MG404 1.8 32.4 1.0
MG A:MG403 2.0 28.4 1.0
MG A:MG405 2.5 41.0 1.0
O A:HOH517 2.6 24.8 1.0
O A:HOH513 2.7 31.5 1.0
O A:HOH604 2.8 39.4 1.0
O A:HOH512 2.8 25.2 1.0
O A:HOH521 2.9 32.1 1.0
O A:HOH569 3.0 31.7 1.0
OE1 A:GLU66 3.1 20.6 1.0
OE2 A:GLU66 3.2 20.3 1.0
O A:HOH509 3.3 43.6 1.0
CD A:GLU66 3.6 19.1 1.0
O A:HOH507 3.7 47.0 1.0
OE2 A:GLU69 4.0 29.7 1.0
O A:HOH542 4.0 31.1 1.0
OE1 A:GLU70 4.2 19.2 1.0
O A:HOH515 4.4 40.9 1.0
MG A:MG402 4.5 21.4 1.0
O32 A:YUT401 4.6 22.2 1.0
CA A:GLY51 4.9 12.9 1.0
N A:GLY52 4.9 14.4 1.0
O23 A:YUT401 4.9 33.5 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 19:41:19 2024

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