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Fluorine in PDB 6cz4: Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide

Enzymatic activity of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide

All present enzymatic activity of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide:
2.7.10.2;

Protein crystallography data

The structure of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide, PDB code: 6cz4 was solved by K.S.Gajiwala, E.Johnson, C.N.Cronin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.82 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 37.914, 54.873, 134.629, 90.00, 90.00, 90.00
R / Rfree (%) 25.4 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide (pdb code 6cz4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide, PDB code: 6cz4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6cz4

Go back to Fluorine Binding Sites List in 6cz4
Fluorine binding site 1 out of 4 in the Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:27.2
occ:1.00
 F31 A:FKY9001 0.0 27.2 1.0
C30 A:FKY9001 1.4 27.9 1.0
F32 A:FKY9001 2.2 27.5 1.0
F33 A:FKY9001 2.2 29.4 1.0
O29 A:FKY9001 2.3 25.6 1.0
C26 A:FKY9001 2.9 22.6 1.0
C25 A:FKY9001 3.1 21.7 1.0
NE2 A:HIS310 3.3 18.5 1.0
CD2 A:HIS310 3.3 18.5 1.0
O A:HOH9186 3.4 27.1 1.0
O A:GLY329 3.7 17.6 1.0
C A:GLY329 3.8 18.2 1.0
O A:HOH9202 4.0 29.2 1.0
C27 A:FKY9001 4.0 23.4 1.0
CB A:ASP330 4.1 20.7 1.0
CA A:GLY329 4.1 16.8 1.0
C24 A:FKY9001 4.3 22.1 1.0
CE1 A:HIS310 4.3 19.0 1.0
N A:ASP330 4.3 18.7 1.0
CG A:HIS310 4.4 17.8 1.0
CE2 A:TYR308 4.5 22.4 1.0
CG1 A:VAL328 4.6 17.7 1.0
O A:VAL328 4.7 18.3 1.0
N A:GLY329 4.8 16.3 1.0
CA A:ASP330 4.8 19.3 1.0
ND1 A:HIS310 4.9 19.8 1.0
C A:VAL328 4.9 17.8 1.0
C28 A:FKY9001 5.0 23.3 1.0
CD1 A:LEU303 5.0 18.2 1.0

Fluorine binding site 2 out of 4 in 6cz4

Go back to Fluorine Binding Sites List in 6cz4
Fluorine binding site 2 out of 4 in the Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:27.5
occ:1.00
 F32 A:FKY9001 0.0 27.5 1.0
C30 A:FKY9001 1.3 27.9 1.0
F33 A:FKY9001 2.2 29.4 1.0
F31 A:FKY9001 2.2 27.2 1.0
O29 A:FKY9001 2.3 25.6 1.0
CD1 A:LEU242 3.5 23.3 1.0
C26 A:FKY9001 3.5 22.6 1.0
CE2 A:TYR308 3.6 22.4 1.0
CD1 A:LEU303 3.7 18.2 1.0
CD2 A:LEU303 3.7 20.4 1.0
CD2 A:TYR308 3.9 21.6 1.0
CD2 A:HIS310 4.1 18.5 1.0
CG2 A:ILE247 4.3 19.7 1.0
O A:HOH9186 4.3 27.1 1.0
CG A:LEU303 4.3 19.2 1.0
C25 A:FKY9001 4.4 21.7 1.0
CZ A:TYR308 4.4 22.8 1.0
C27 A:FKY9001 4.4 23.4 1.0
OH A:TYR308 4.7 25.9 1.0
NE2 A:HIS310 4.7 18.5 1.0
CD1 A:ILE247 4.9 19.7 1.0
CG A:LEU242 4.9 21.4 1.0
CG A:TYR308 5.0 21.6 1.0

Fluorine binding site 3 out of 4 in 6cz4

Go back to Fluorine Binding Sites List in 6cz4
Fluorine binding site 3 out of 4 in the Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:29.4
occ:1.00
 F33 A:FKY9001 0.0 29.4 1.0
C30 A:FKY9001 1.4 27.9 1.0
F32 A:FKY9001 2.2 27.5 1.0
F31 A:FKY9001 2.2 27.2 1.0
O29 A:FKY9001 2.3 25.6 1.0
C26 A:FKY9001 2.8 22.6 1.0
O A:VAL328 3.0 18.3 1.0
C27 A:FKY9001 3.2 23.4 1.0
CG2 A:ILE247 3.5 19.7 1.0
C A:VAL328 3.7 17.8 1.0
CA A:GLY329 3.7 16.8 1.0
C25 A:FKY9001 3.8 21.7 1.0
N A:GLY329 4.0 16.3 1.0
CG1 A:VAL328 4.2 17.7 1.0
C A:GLY329 4.2 18.2 1.0
O A:GLY329 4.3 17.6 1.0
C28 A:FKY9001 4.4 23.3 1.0
CB A:VAL328 4.5 16.8 1.0
CD1 A:ILE247 4.5 19.7 1.0
N A:LEU248 4.5 18.9 1.0
CD2 A:HIS310 4.6 18.5 1.0
CB A:ILE247 4.7 17.9 1.0
NE2 A:HIS310 4.7 18.5 1.0
CA A:VAL328 4.7 16.9 1.0
O A:LEU248 4.7 21.4 1.0
CD1 A:LEU303 4.8 18.2 1.0
C24 A:FKY9001 4.8 22.1 1.0
CD1 A:LEU242 4.8 23.3 1.0
CA A:ILE247 4.9 18.5 1.0
N A:ASP330 5.0 18.7 1.0

Fluorine binding site 4 out of 4 in 6cz4

Go back to Fluorine Binding Sites List in 6cz4
Fluorine binding site 4 out of 4 in the Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the PTK6 Kinase Domain Bound to A Type II Inhibitor 2- {[(3R,4S)-3-Fluoro-1-{[4-(Trifluoromethoxy)Phenyl]Acetyl}Piperidin-4- Yl]Oxy}-5-(1-Methyl-1H-Imidazol-4-Yl)Pyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F9001

b:21.7
occ:1.00
 F34 A:FKY9001 0.0 21.7 1.0
C15 A:FKY9001 1.4 22.2 1.0
C14 A:FKY9001 2.4 21.1 1.0
C16 A:FKY9001 2.4 21.6 1.0
O13 A:FKY9001 2.7 22.0 1.0
N17 A:FKY9001 2.7 21.8 1.0
C19 A:FKY9001 3.0 21.6 1.0
OG1 A:THR264 3.1 22.9 1.0
C20 A:FKY9001 3.2 22.6 1.0
O A:HOH9224 3.3 23.4 1.0
CD2 A:LEU248 3.3 23.0 1.0
CG2 A:THR264 3.4 24.6 1.0
C22 A:FKY9001 3.4 23.2 1.0
C18 A:FKY9001 3.5 22.1 1.0
N36 A:FKY9001 3.5 20.5 1.0
CB A:THR264 3.8 22.2 1.0
C10 A:FKY9001 4.0 19.3 1.0
O21 A:FKY9001 4.1 22.2 1.0
CG A:LEU248 4.5 20.4 1.0
C35 A:FKY9001 4.6 20.0 1.0
C9 A:FKY9001 4.7 18.8 1.0
C23 A:FKY9001 4.8 22.0 1.0
N11 A:FKY9001 4.9 19.5 1.0

Reference:

L.Qiu, K.Levine, K.S.Gajiwala, C.N.Cronin, A.Nagata, E.Johnson, M.Kraus, J.Tatlock, R.Kania, T.Foley, S.Sun. Small Molecule Inhibitors Reveal PTK6 Kinase Is Not An Oncogenic Driver in Breast Cancers. Plos One V. 13 98374 2018.
ISSN: ESSN 1932-6203
PubMed: 29879184
DOI: 10.1371/JOURNAL.PONE.0198374
Page generated: Thu Aug 1 18:43:35 2024

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