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Fluorine in PDB 5kmk: Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide

Enzymatic activity of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide

All present enzymatic activity of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide:
2.7.10.1;

Protein crystallography data

The structure of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide, PDB code: 5kmk was solved by H.P.Su, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.30 / 2.24
Space group P 31 1 2
Cell size a, b, c (Å), α, β, γ (°) 52.307, 52.307, 224.886, 90.00, 90.00, 120.00
R / Rfree (%) 22.4 / 28.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide (pdb code 5kmk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide, PDB code: 5kmk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 5kmk

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Fluorine binding site 1 out of 5 in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:51.4
occ:1.00
 F4 A:6UG901 0.0 51.4 1.0
C17 A:6UG901 1.4 48.3 1.0
C16 A:6UG901 2.3 47.2 1.0
C18 A:6UG901 2.4 46.3 1.0
SD A:MET587 3.2 51.4 1.0
CD1 A:LEU564 3.2 49.7 1.0
CZ A:PHE589 3.5 35.7 1.0
C15 A:6UG901 3.6 47.6 1.0
C19 A:6UG901 3.6 45.8 1.0
CE A:LYS544 4.0 57.6 1.0
CD A:LYS544 4.0 54.5 1.0
CE A:MET587 4.0 48.9 1.0
C14 A:6UG901 4.1 46.5 1.0
CD1 A:LEU486 4.3 67.3 1.0
CE1 A:PHE589 4.3 35.8 1.0
CG A:LEU564 4.5 50.0 1.0
CE2 A:PHE589 4.5 37.2 1.0
CG A:MET587 4.6 45.3 1.0
CD2 A:LEU564 4.6 49.5 1.0
OE2 A:GLU560 4.7 77.2 1.0
CB A:MET587 4.9 40.5 1.0

Fluorine binding site 2 out of 5 in 5kmk

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Fluorine binding site 2 out of 5 in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:57.3
occ:1.00
 F A:6UG901 0.0 57.3 1.0
C11 A:6UG901 1.4 56.1 1.0
C10 A:6UG901 2.3 57.3 1.0
C6 A:6UG901 2.4 52.3 1.0
C5 A:6UG901 2.9 53.7 1.0
O A:6UG901 2.9 56.4 1.0
O A:HOH1008 3.1 39.9 1.0
CA A:GLY485 3.5 66.3 1.0
CE1 A:PHE646 3.5 62.8 1.0
C7 A:6UG901 3.6 52.6 1.0
C9 A:6UG901 3.6 58.0 1.0
CZ A:PHE646 3.7 61.3 1.0
C A:GLY485 3.7 69.3 1.0
N A:LEU486 3.7 65.2 1.0
NE2 A:HIS648 3.8 43.3 1.0
O A:HIS648 3.8 46.9 1.0
CD2 A:HIS648 3.9 43.7 1.0
N A:6UG901 3.9 49.6 1.0
CE1 A:HIS648 4.0 43.2 1.0
CG A:HIS648 4.1 44.1 1.0
C8 A:6UG901 4.1 54.5 1.0
ND1 A:HIS648 4.2 44.5 1.0
CA A:HIS648 4.3 42.9 1.0
CG A:LEU486 4.4 67.7 1.0
O A:GLY485 4.4 68.4 1.0
O A:HOH1028 4.5 47.4 1.0
C A:HIS648 4.6 46.9 1.0
CA A:LEU486 4.7 64.5 1.0
N A:GLY485 4.7 67.6 1.0
CB A:HIS648 4.8 42.3 1.0
CD1 A:PHE646 4.8 62.6 1.0
C12 A:6UG901 4.8 62.9 1.0
F2 A:6UG901 5.0 66.8 1.0
O A:SER484 5.0 73.3 1.0
CB A:LEU486 5.0 64.1 1.0

Fluorine binding site 3 out of 5 in 5kmk

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Fluorine binding site 3 out of 5 in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:62.9
occ:1.00
 F3 A:6UG901 0.0 62.9 1.0
C12 A:6UG901 1.3 62.9 1.0
F2 A:6UG901 2.1 66.8 1.0
F1 A:6UG901 2.2 64.2 1.0
C9 A:6UG901 2.3 58.0 1.0
C8 A:6UG901 3.1 54.5 1.0
C10 A:6UG901 3.2 57.3 1.0
CG2 A:ILE572 3.6 43.5 1.0
CD1 A:LEU567 3.6 67.0 1.0
CB A:LEU567 4.2 61.8 1.0
CD1 A:ILE572 4.2 51.9 1.0
C7 A:6UG901 4.4 52.6 1.0
C11 A:6UG901 4.4 56.1 1.0
CG A:LEU567 4.5 66.7 1.0
CD2 A:LEU564 4.6 49.5 1.0
CD2 A:LEU641 4.7 58.8 1.0
CB A:ILE572 4.8 45.2 1.0
CG1 A:ILE572 4.9 45.1 1.0
C6 A:6UG901 4.9 52.3 1.0
CD2 A:LEU486 5.0 68.4 1.0

Fluorine binding site 4 out of 5 in 5kmk

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Fluorine binding site 4 out of 5 in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:66.8
occ:1.00
 F2 A:6UG901 0.0 66.8 1.0
C12 A:6UG901 1.3 62.9 1.0
F3 A:6UG901 2.1 62.9 1.0
F1 A:6UG901 2.1 64.2 1.0
C9 A:6UG901 2.4 58.0 1.0
C10 A:6UG901 2.8 57.3 1.0
CG2 A:ILE666 3.3 42.3 1.0
CD1 A:ILE572 3.4 51.9 1.0
CD1 A:LEU641 3.4 59.2 1.0
C8 A:6UG901 3.6 54.5 1.0
CD2 A:LEU641 4.0 58.8 1.0
C11 A:6UG901 4.1 56.1 1.0
CG A:LEU641 4.2 59.5 1.0
CD2 A:HIS648 4.3 43.7 1.0
CG2 A:ILE572 4.4 43.5 1.0
CB A:ILE666 4.4 43.2 1.0
NE2 A:HIS648 4.6 43.3 1.0
O A:ILE666 4.6 44.1 1.0
CG1 A:ILE572 4.7 45.1 1.0
CE1 A:PHE646 4.8 62.8 1.0
C A:ILE666 4.8 44.7 1.0
C7 A:6UG901 4.8 52.6 1.0
O A:HOH1012 4.9 35.3 1.0
F A:6UG901 5.0 57.3 1.0
CD1 A:LEU567 5.0 67.0 1.0

Fluorine binding site 5 out of 5 in 5kmk

Go back to Fluorine Binding Sites List in 5kmk
Fluorine binding site 5 out of 5 in the Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Trka Jm-Kinase with 2-Fluoro-{N}-[2-(4-Fluorophenyl)-6-Methyl-3- Pyridyl]-4-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:64.2
occ:1.00
 F1 A:6UG901 0.0 64.2 1.0
C12 A:6UG901 1.3 62.9 1.0
F2 A:6UG901 2.1 66.8 1.0
F3 A:6UG901 2.2 62.9 1.0
C9 A:6UG901 2.4 58.0 1.0
C8 A:6UG901 2.9 54.5 1.0
O A:ILE666 3.1 44.1 1.0
C A:ILE666 3.5 44.7 1.0
C10 A:6UG901 3.6 57.3 1.0
CG2 A:ILE666 3.6 42.3 1.0
CA A:GLY667 3.6 41.4 1.0
CG2 A:ILE572 3.7 43.5 1.0
N A:GLY667 3.8 41.8 1.0
CD1 A:ILE572 4.0 51.9 1.0
C7 A:6UG901 4.2 52.6 1.0
CB A:ILE666 4.4 43.2 1.0
O A:HOH1012 4.4 35.3 1.0
N A:VAL573 4.5 44.5 1.0
CA A:ILE666 4.6 39.5 1.0
CB A:ILE572 4.6 45.2 1.0
C11 A:6UG901 4.7 56.1 1.0
CA A:ILE572 4.7 43.8 1.0
CG1 A:ILE572 4.9 45.1 1.0
C A:GLY667 4.9 43.4 1.0

Reference:

H.P.Su, K.Rickert, C.Burlein, K.Narayan, M.Bukhtiyarova, D.M.Hurzy, C.A.Stump, X.Zhang, J.Reid, A.Krasowska-Zoladek, S.Tummala, J.M.Shipman, M.Kornienko, P.A.Lemaire, D.Krosky, A.Heller, A.Achab, C.Chamberlin, P.Saradjian, B.Sauvagnat, X.Yang, M.R.Ziebell, E.Nickbarg, J.M.Sanders, M.T.Bilodeau, S.S.Carroll, K.J.Lumb, S.M.Soisson, D.A.Henze, A.J.Cooke. Structural Characterization of Nonactive Site, Trka-Selective Kinase Inhibitors. Proc. Natl. Acad. Sci. V. 114 E297 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28039433
DOI: 10.1073/PNAS.1611577114
Page generated: Thu Aug 1 11:07:07 2024

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