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Fluorine in PDB 5v82: PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine)

Enzymatic activity of PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine)

All present enzymatic activity of PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine):
2.7.11.1;

Protein crystallography data

The structure of PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine), PDB code: 5v82 was solved by J.M.Murray, H.Wallweber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.78 / 1.89
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 96.485, 96.485, 80.628, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 19.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine) (pdb code 5v82). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine), PDB code: 5v82:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5v82

Go back to Fluorine Binding Sites List in 5v82
Fluorine binding site 1 out of 2 in the PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:47.1
occ:1.00
 F29 A:96Y401 0.0 47.1 1.0
C28 A:96Y401 1.4 46.2 1.0
F30 A:96Y401 2.3 51.2 1.0
C23 A:96Y401 2.4 34.4 1.0
C27 A:96Y401 2.4 46.8 1.0
C21 A:96Y401 2.8 35.5 1.0
C24 A:96Y401 2.9 40.1 1.0
C26 A:96Y401 3.0 45.8 1.0
N22 A:96Y401 3.1 35.6 1.0
N25 A:96Y401 3.5 35.9 1.0
C20 A:96Y401 3.8 36.7 1.0
O A:LEU44 3.8 43.8 1.0
C A:LEU44 3.9 47.8 1.0
CB A:LEU44 3.9 44.2 1.0
N A:GLY45 4.0 48.2 1.0
CA A:GLY45 4.1 43.1 1.0
C17 A:96Y401 4.1 29.9 1.0
C9 A:96Y401 4.3 28.0 1.0
N7 A:96Y401 4.5 34.5 1.0
CA A:LEU44 4.6 40.1 1.0
C1 A:96Y401 4.7 41.0 1.0
C19 A:96Y401 4.8 34.7 1.0
CB A:VAL52 4.8 30.7 1.0
C A:GLY45 4.9 49.8 1.0
O A:HOH583 4.9 57.1 1.0
C18 A:96Y401 4.9 33.5 1.0
CG1 A:VAL52 4.9 34.7 1.0
N16 A:96Y401 5.0 30.3 1.0
C10 A:96Y401 5.0 26.5 1.0

Fluorine binding site 2 out of 2 in 5v82

Go back to Fluorine Binding Sites List in 5v82
Fluorine binding site 2 out of 2 in the PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PIM1 Kinase in Complex with CPD17 (1-(6-(4,4-Difluoropiperidin-3-Yl) Pyridin-2-Yl)-6-(6-Methylpyrazin-2-Yl)-1H-Pyrazolo[4,3-C]Pyridine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:51.2
occ:1.00
 F30 A:96Y401 0.0 51.2 1.0
C28 A:96Y401 1.4 46.2 1.0
F29 A:96Y401 2.3 47.1 1.0
C23 A:96Y401 2.4 34.4 1.0
C27 A:96Y401 2.4 46.8 1.0
O A:LEU44 2.7 43.8 1.0
C21 A:96Y401 2.9 35.5 1.0
C20 A:96Y401 3.0 36.7 1.0
O A:HOH611 3.2 59.4 1.0
C A:LEU44 3.5 47.8 1.0
O A:HOH583 3.7 57.1 1.0
C24 A:96Y401 3.7 40.1 1.0
C26 A:96Y401 3.7 45.8 1.0
N22 A:96Y401 3.9 35.6 1.0
CB A:LEU44 3.9 44.2 1.0
N25 A:96Y401 4.1 35.9 1.0
CA A:LEU44 4.2 40.1 1.0
C19 A:96Y401 4.2 34.7 1.0
N A:GLY45 4.2 48.2 1.0
CA A:GLY45 4.4 43.1 1.0
O A:HOH559 4.7 44.8 1.0
C17 A:96Y401 4.8 29.9 1.0
OD1 A:ASP128 4.8 44.0 1.0
C18 A:96Y401 5.0 33.5 1.0

Reference:

X.Wang, A.Kolesnikov, S.Tay, G.Chan, Q.Chao, S.Do, J.Drummond, A.J.Ebens, N.Liu, J.Ly, E.Harstad, H.Hu, J.Moffat, V.Munugalavadla, J.Murray, D.Slaga, V.Tsui, M.Volgraf, H.Wallweber, J.H.Chang. Discovery of 5-Azaindazole (Gne-955) As A Potent Pan-Pim Inhibitor with Optimized Bioavailability. J. Med. Chem. V. 60 4458 2017.
ISSN: ISSN 1520-4804
PubMed: 28445037
DOI: 10.1021/ACS.JMEDCHEM.7B00418
Page generated: Tue Jul 15 08:30:03 2025

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