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Fluorine in PDB 5dwr: Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies

Enzymatic activity of Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies

All present enzymatic activity of Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies:
2.7.11.1;

Protein crystallography data

The structure of Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies, PDB code: 5dwr was solved by C.Bellamacina, D.Bussiere, M.Burger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.44 / 2.00
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 98.233, 98.233, 81.123, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 20.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies (pdb code 5dwr). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies, PDB code: 5dwr:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5dwr

Go back to Fluorine Binding Sites List in 5dwr
Fluorine binding site 1 out of 3 in the Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.0
occ:1.00
 F2 A:5H7401 0.0 30.0 1.0
C23 A:5H7401 1.4 29.7 1.0
C18 A:5H7401 2.3 27.6 1.0
C22 A:5H7401 2.3 28.6 1.0
H A:5H7401 2.5 23.2 1.0
H22 A:5H7401 2.6 28.5 1.0
H1 A:5H7401 2.6 18.7 1.0
H2 A:5H7401 2.7 20.9 1.0
N3 A:5H7401 2.8 23.8 1.0
C17 A:5H7401 2.8 24.6 1.0
CD2 A:LEU174 3.0 34.7 1.0
CD1 A:ILE185 3.4 24.4 1.0
C1 A:5H7401 3.5 23.6 1.0
C3 A:5H7401 3.6 19.1 1.0
H17 A:5H7401 3.6 23.9 1.0
C19 A:5H7401 3.6 27.1 1.0
C21 A:5H7401 3.6 28.8 1.0
CD1 A:LEU174 3.7 33.0 1.0
C5 A:5H7401 3.7 20.8 1.0
CG A:LEU174 3.8 31.7 1.0
C2 A:5H7401 3.9 22.4 1.0
C13 A:5H7401 3.9 24.1 1.0
H7 A:5H7401 4.0 22.2 1.0
C16 A:5H7401 4.0 25.6 1.0
C6 A:5H7401 4.1 23.3 1.0
C20 A:5H7401 4.1 26.3 1.0
N2 A:5H7401 4.1 23.6 1.0
C4 A:5H7401 4.2 18.7 1.0
H12 A:5H7401 4.3 22.2 1.0
H21 A:5H7401 4.5 29.7 1.0
H11 A:5H7401 4.5 20.5 1.0
C12 A:5H7401 4.5 25.1 1.0
C A:5H7401 4.6 28.5 1.0
F A:5H7401 4.6 27.1 1.0
N A:5H7401 4.7 18.7 1.0
F1 A:5H7401 4.7 27.1 1.0
CB A:ASP128 4.7 20.8 1.0
H3 A:5H7401 4.8 28.6 1.0
H5 A:5H7401 4.8 28.2 1.0
C7 A:5H7401 4.8 19.3 1.0
H9 A:5H7401 4.8 19.7 1.0
C14 A:5H7401 4.9 24.5 1.0
C15 A:5H7401 4.9 25.4 1.0
CG1 A:ILE185 4.9 20.6 1.0
H6 A:5H7401 4.9 21.9 1.0
C11 A:5H7401 5.0 20.6 1.0

Fluorine binding site 2 out of 3 in 5dwr

Go back to Fluorine Binding Sites List in 5dwr
Fluorine binding site 2 out of 3 in the Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.1
occ:1.00
 F1 A:5H7401 0.0 27.1 1.0
C19 A:5H7401 1.4 27.1 1.0
C20 A:5H7401 2.3 26.3 1.0
C18 A:5H7401 2.3 27.6 1.0
H20 A:5H7401 2.6 26.5 1.0
F A:5H7401 2.7 27.1 1.0
C17 A:5H7401 2.8 24.6 1.0
C16 A:5H7401 3.0 25.6 1.0
CD1 A:LEU44 3.3 30.3 1.0
CD A:ARG122 3.3 31.1 1.0
C23 A:5H7401 3.6 29.7 1.0
C21 A:5H7401 3.6 28.8 1.0
CG A:ARG122 3.6 27.6 1.0
O A:HOH729 3.9 36.1 1.0
N3 A:5H7401 3.9 23.8 1.0
C22 A:5H7401 4.1 28.6 1.0
CG1 A:VAL126 4.1 30.0 1.0
C15 A:5H7401 4.1 25.4 1.0
CB A:ARG122 4.5 24.6 1.0
H21 A:5H7401 4.5 29.7 1.0
CB A:ALA65 4.5 22.1 1.0
CG A:LEU44 4.6 29.9 1.0
O A:HOH627 4.6 31.2 1.0
F2 A:5H7401 4.7 30.0 1.0
H19 A:5H7401 4.7 25.0 1.0
CD2 A:LEU44 4.7 33.4 1.0
NE A:ARG122 4.7 29.8 1.0
C13 A:5H7401 4.8 24.1 1.0
C14 A:5H7401 4.9 24.5 1.0

Fluorine binding site 3 out of 3 in 5dwr

Go back to Fluorine Binding Sites List in 5dwr
Fluorine binding site 3 out of 3 in the Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin- 3-Yl)-6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1,2 and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:27.1
occ:1.00
 F A:5H7401 0.0 27.1 1.0
C16 A:5H7401 1.4 25.6 1.0
C15 A:5H7401 2.4 25.4 1.0
C17 A:5H7401 2.4 24.6 1.0
H19 A:5H7401 2.6 25.0 1.0
F1 A:5H7401 2.7 27.1 1.0
C18 A:5H7401 2.9 27.6 1.0
C19 A:5H7401 3.0 27.1 1.0
CD1 A:LEU174 3.4 33.0 1.0
CD A:PRO123 3.5 33.8 1.0
CG A:ARG122 3.6 27.6 1.0
C14 A:5H7401 3.6 24.5 1.0
N3 A:5H7401 3.6 23.8 1.0
CA A:ARG122 3.8 25.8 1.0
CB A:ARG122 3.9 24.6 1.0
CG1 A:VAL126 4.0 30.0 1.0
C23 A:5H7401 4.0 29.7 1.0
C13 A:5H7401 4.1 24.1 1.0
C20 A:5H7401 4.2 26.3 1.0
O A:GLU121 4.2 28.6 1.0
N A:PRO123 4.2 31.3 1.0
CG2 A:VAL126 4.3 30.4 1.0
CD A:ARG122 4.4 31.1 1.0
C A:ARG122 4.4 31.8 1.0
H18 A:5H7401 4.5 23.5 1.0
CB A:VAL126 4.6 29.9 1.0
O A:PRO123 4.6 33.5 1.0
F2 A:5H7401 4.6 30.0 1.0
H20 A:5H7401 4.7 26.5 1.0
CB A:ALA65 4.7 22.1 1.0
CG A:LEU174 4.8 31.7 1.0
CG A:PRO123 4.8 37.9 1.0
CD1 A:ILE104 4.9 41.6 1.0
N A:ARG122 4.9 25.9 1.0
C22 A:5H7401 5.0 28.6 1.0

Reference:

M.T.Burger, G.Nishiguchi, W.Han, J.Lan, R.Simmons, G.Atallah, Y.Ding, V.Tamez, Y.Zhang, M.Mathur, K.Muller, C.Bellamacina, M.K.Lindvall, R.Zang, K.Huh, P.Feucht, T.Zavorotinskaya, Y.Dai, S.Basham, J.Chan, E.Ginn, A.Aycinena, J.Holash, J.Castillo, J.L.Langowski, Y.Wang, M.Y.Chen, A.Lambert, C.Fritsch, A.Kauffmann, E.Pfister, K.G.Vanasse, P.D.Garcia. Identification of N-(4-((1R,3S,5S)-3-Amino-5-Methylcyclohexyl)Pyridin-3-Yl) -6-(2,6-Difluorophenyl)-5-Fluoropicolinamide (PIM447), A Potent and Selective Proviral Insertion Site of Moloney Murine Leukemia (Pim) 1, 2, and 3 Kinase Inhibitor in Clinical Trials For Hematological Malignancies. J.Med.Chem. V. 58 8373 2015.
ISSN: ISSN 0022-2623
PubMed: 26505898
DOI: 10.1021/ACS.JMEDCHEM.5B01275
Page generated: Thu Aug 1 08:54:31 2024

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