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Fluorine in PDB 4jx7: Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One

Enzymatic activity of Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One

All present enzymatic activity of Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One, PDB code: 4jx7 was solved by S.J.Lee, B.G.Han, J.W.Cho, J.S.Choi, J.K.Lee, H.J.Song, J.S.Koh, B.I.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 97.657, 97.657, 81.106, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 22.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One (pdb code 4jx7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One, PDB code: 4jx7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4jx7

Go back to Fluorine Binding Sites List in 4jx7
Fluorine binding site 1 out of 3 in the Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:66.6
occ:1.00
 FAC A:1N6401 0.0 66.6 1.0
CBD A:1N6401 1.4 62.3 1.0
FAD A:1N6401 2.2 69.4 1.0
CAV A:1N6401 2.3 57.9 1.0
FAE A:1N6401 2.3 63.9 1.0
CAI A:1N6401 2.6 54.0 1.0
CAK A:1N6401 3.6 52.0 1.0
CAF A:1N6401 4.0 55.1 1.0
O A:VAL126 4.0 33.2 1.0
OD2 A:ASP128 4.5 51.0 1.0
CA A:GLN127 4.6 29.5 1.0
CAU A:1N6401 4.7 47.2 1.0
OD2 A:ASP131 4.8 45.0 1.0
CAH A:1N6401 4.9 50.5 1.0
N A:ASP128 4.9 28.9 1.0
C A:VAL126 5.0 31.5 1.0

Fluorine binding site 2 out of 3 in 4jx7

Go back to Fluorine Binding Sites List in 4jx7
Fluorine binding site 2 out of 3 in the Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:69.4
occ:1.00
 FAD A:1N6401 0.0 69.4 1.0
CBD A:1N6401 1.3 62.3 1.0
FAC A:1N6401 2.2 66.6 1.0
FAE A:1N6401 2.2 63.9 1.0
CAV A:1N6401 2.2 57.9 1.0
CAK A:1N6401 2.7 52.0 1.0
OD2 A:ASP128 3.1 51.0 1.0
N A:ASP128 3.3 28.9 1.0
CAI A:1N6401 3.4 54.0 1.0
CA A:GLN127 3.8 29.5 1.0
CG A:ASP128 3.9 42.0 1.0
C A:GLN127 4.0 30.1 1.0
CB A:ASP128 4.0 35.3 1.0
CAU A:1N6401 4.1 47.2 1.0
CAO A:1N6401 4.2 44.1 1.0
CA A:ASP128 4.2 30.7 1.0
CAM A:1N6401 4.3 42.9 1.0
O A:VAL126 4.3 33.2 1.0
OD2 A:ASP131 4.5 45.0 1.0
CAF A:1N6401 4.6 55.1 1.0
N A:GLN127 4.7 30.9 1.0
C A:VAL126 4.7 31.5 1.0
CD2 A:LEU174 4.8 27.8 1.0
CG A:GLN127 4.8 29.9 1.0
CAH A:1N6401 4.8 50.5 1.0
CB A:GLN127 4.8 28.5 1.0
N1 A:1N6401 4.9 40.2 1.0
NAR A:1N6401 5.0 43.0 1.0
CG1 A:VAL126 5.0 30.6 1.0

Fluorine binding site 3 out of 3 in 4jx7

Go back to Fluorine Binding Sites List in 4jx7
Fluorine binding site 3 out of 3 in the Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of PIM1 Kinase in Complex with Inhibitor 2-[(Trans- 4-Aminocyclohexyl)Amino]-4-{[3-(Trifluoromethyl) Phenyl]Amino}Pyrido[4,3-D]Pyrimidin-5(6H)-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:63.9
occ:1.00
 FAE A:1N6401 0.0 63.9 1.0
CBD A:1N6401 1.4 62.3 1.0
FAD A:1N6401 2.2 69.4 1.0
CAV A:1N6401 2.3 57.9 1.0
FAC A:1N6401 2.3 66.6 1.0
CAK A:1N6401 3.0 52.0 1.0
CAI A:1N6401 3.3 54.0 1.0
CAO A:1N6401 3.8 44.1 1.0
CAM A:1N6401 3.8 42.9 1.0
CBB A:1N6401 3.9 43.6 1.0
OD2 A:ASP128 4.2 51.0 1.0
CAU A:1N6401 4.2 47.2 1.0
CAF A:1N6401 4.4 55.1 1.0
OD2 A:ASP131 4.6 45.0 1.0
NAA A:1N6401 4.7 41.4 1.0
N1 A:1N6401 4.7 40.2 1.0
O A:LEU44 4.8 31.5 1.0
CAH A:1N6401 4.8 50.5 1.0
CAN A:1N6401 4.8 43.7 1.0
CBC A:1N6401 4.9 42.2 1.0
CAL A:1N6401 5.0 43.9 1.0

Reference:

S.J.Lee, B.G.Han, J.W.Cho, J.S.Choi, J.Lee, H.J.Song, J.S.Koh, B.I.Lee. Crystal Structure of PIM1 Kinase in Complex with A Pyrido[4,3-D]Pyrimidine Derivative Suggests A Unique Binding Mode. Plos One V. 8 70358 2013.
ISSN: ESSN 1932-6203
PubMed: 23936194
DOI: 10.1371/JOURNAL.PONE.0070358
Page generated: Thu Aug 1 03:02:20 2024

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