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Fluorine in PDB 6no9: PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide)

Enzymatic activity of PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide)

All present enzymatic activity of PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide):
2.7.11.1;

Protein crystallography data

The structure of PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide), PDB code: 6no9 was solved by J.M.Murray, C.Noland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.84 / 1.71
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 96.632, 96.632, 80.703, 90.00, 90.00, 120.00
R / Rfree (%) 16.8 / 20.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide) (pdb code 6no9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide), PDB code: 6no9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6no9

Go back to Fluorine Binding Sites List in 6no9
Fluorine binding site 1 out of 3 in the PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:36.3
occ:1.00
 F21 A:KUV504 0.0 36.3 1.0
C20 A:KUV504 1.3 33.8 1.0
C19 A:KUV504 2.4 32.4 1.0
C15 A:KUV504 2.4 33.3 1.0
S12 A:KUV504 2.8 33.5 1.0
C13 A:KUV504 2.8 32.1 1.0
CD A:ARG122 3.4 38.4 1.0
CG A:ARG122 3.4 36.7 1.0
CD1 A:LEU44 3.5 47.6 1.0
CG1 A:VAL126 3.6 41.4 1.0
C18 A:KUV504 3.6 36.5 1.0
C16 A:KUV504 3.6 34.2 1.0
O A:HOH633 4.1 42.6 1.0
N14 A:KUV504 4.1 31.8 1.0
C17 A:KUV504 4.1 36.7 1.0
CD2 A:LEU44 4.2 52.9 1.0
CB A:ARG122 4.5 37.7 1.0
C11 A:KUV504 4.5 30.9 1.0
CG A:LEU44 4.5 51.3 1.0
F22 A:KUV504 4.8 33.7 1.0
CD1 A:LEU174 4.8 41.1 1.0
NE A:ARG122 4.8 40.1 1.0
C10 A:KUV504 4.8 29.3 1.0
O A:PRO123 4.9 44.4 1.0
CB A:VAL126 4.9 39.7 1.0

Fluorine binding site 2 out of 3 in 6no9

Go back to Fluorine Binding Sites List in 6no9
Fluorine binding site 2 out of 3 in the PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:33.7
occ:1.00
 F22 A:KUV504 0.0 33.7 1.0
C16 A:KUV504 1.3 34.2 1.0
C17 A:KUV504 2.4 36.7 1.0
C15 A:KUV504 2.4 33.3 1.0
H28 A:KUV504 2.6 40.1 1.0
N14 A:KUV504 2.8 31.8 1.0
C13 A:KUV504 2.9 32.1 1.0
F33 A:KUV504 3.1 39.0 1.0
CD2 A:LEU174 3.4 43.7 1.0
C27 A:KUV504 3.4 33.2 1.0
CD1 A:ILE185 3.4 25.4 1.0
C29 A:KUV504 3.6 36.0 1.0
C18 A:KUV504 3.6 36.5 1.0
C20 A:KUV504 3.6 33.8 1.0
C31 A:KUV504 3.7 35.3 1.0
N34 A:KUV504 3.7 29.3 1.0
C10 A:KUV504 4.0 29.3 1.0
C19 A:KUV504 4.1 32.4 1.0
N7 A:KUV504 4.2 27.9 1.0
OD2 A:ASP128 4.3 40.7 1.0
CG A:LEU174 4.4 41.6 1.0
CB A:ASP128 4.5 30.7 1.0
N24 A:KUV504 4.6 34.7 1.0
S12 A:KUV504 4.6 33.5 1.0
H30 A:KUV504 4.6 43.4 1.0
C8 A:KUV504 4.7 30.7 1.0
CD1 A:LEU174 4.7 41.1 1.0
C26 A:KUV504 4.7 27.5 1.0
F21 A:KUV504 4.8 36.3 1.0
C32 A:KUV504 4.8 34.0 1.0
CG A:ASP128 4.9 38.7 1.0
C11 A:KUV504 4.9 30.9 1.0
CG1 A:ILE185 5.0 25.3 1.0

Fluorine binding site 3 out of 3 in 6no9

Go back to Fluorine Binding Sites List in 6no9
Fluorine binding site 3 out of 3 in the PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PIM1 in Complex with CPD16 (5-Amino-N-(5-((4R,5R)-4-Amino-5- Fluoroazepan-1-Yl)-1-Methyl-1H-Pyrazol-4-Yl)-2-(2,6-Difluorophenyl) Thiazole-4-Carboxamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:39.0
occ:1.00
 F33 A:KUV504 0.0 39.0 1.0
C29 A:KUV504 1.4 36.0 1.0
H30 A:KUV504 2.1 43.4 1.0
C27 A:KUV504 2.3 33.2 1.0
C31 A:KUV504 2.4 35.3 1.0
N34 A:KUV504 2.6 29.3 1.0
H28 A:KUV504 2.7 40.1 1.0
F22 A:KUV504 3.1 33.7 1.0
O A:HOH634 3.4 61.0 1.0
C17 A:KUV504 3.6 36.7 1.0
O A:LEU44 3.6 56.6 1.0
C16 A:KUV504 3.6 34.2 1.0
C32 A:KUV504 3.7 34.0 1.0
C26 A:KUV504 3.7 27.5 1.0
OD2 A:ASP128 3.8 40.7 1.0
O A:HOH711 3.9 62.5 1.0
O A:HOH662 4.1 43.6 1.0
C A:LEU44 4.2 54.1 1.0
N24 A:KUV504 4.3 34.7 1.0
C25 A:KUV504 4.6 28.1 1.0
CA A:GLY45 4.6 54.6 1.0
N A:GLY45 4.7 53.5 1.0
C18 A:KUV504 4.7 36.5 1.0
CB A:LEU44 4.7 51.1 1.0
C15 A:KUV504 4.8 33.3 1.0
O A:HOH720 4.8 54.1 1.0
CG A:ASP128 4.9 38.7 1.0

Reference:

X.Wang, W.Blackaby, V.Allen, G.K.Y.Chan, J.H.Chang, P.C.Chiang, C.Diene, J.Drummond, S.Do, E.Fan, E.B.Harstad, A.Hodges, H.Hu, W.Jia, W.Kofie, A.Kolesnikov, J.P.Lyssikatos, J.Ly, M.Matteucci, J.G.Moffat, V.Munugalavadla, J.Murray, D.Nash, C.L.Noland, G.Del Rosario, L.Ross, C.Rouse, A.Sharpe, D.Slaga, M.Sun, V.Tsui, H.Wallweber, S.F.Yu, A.J.Ebens. Optimization of Pan-Pim Kinase Activity and Oral Bioavailability Leading to Diaminopyrazole (Gdc-0339) For the Treatment of Multiple Myeloma. J. Med. Chem. V. 62 2140 2019.
ISSN: ISSN 1520-4804
PubMed: 30715878
DOI: 10.1021/ACS.JMEDCHEM.8B01857
Page generated: Thu Aug 1 23:12:19 2024

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