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Fluorine in PDB 3we4: Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole

Enzymatic activity of Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole

All present enzymatic activity of Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole, PDB code: 3we4 was solved by H.Niwa, M.Shirouzu, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.47 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 70.930, 70.930, 146.861, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.1

Other elements in 3we4:

The structure of Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole (pdb code 3we4). 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 S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole, PDB code: 3we4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3we4

Go back to Fluorine Binding Sites List in 3we4
Fluorine binding site 1 out of 3 in the Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole


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 S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:50.6
occ:1.00
 FAB A:5FI402 0.0 50.6 1.0
CBB A:5FI402 1.3 47.5 1.0
FAD A:5FI402 2.1 48.5 1.0
FAC A:5FI402 2.1 51.1 1.0
CAU A:5FI402 2.4 41.2 1.0
CAE A:5FI402 3.0 35.9 1.0
CD2 A:LEU125 3.1 50.5 1.0
CAI A:5FI402 3.4 39.6 1.0
C A:GLY103 3.4 41.8 1.0
CA A:GLY103 3.5 38.0 1.0
N A:GLY103 3.6 44.5 1.0
N A:LYS104 3.6 35.3 1.0
O A:GLY103 3.8 42.5 1.0
C A:TYR102 3.9 45.0 1.0
CE A:LYS123 4.0 51.0 1.0
O A:VAL124 4.1 43.7 1.0
O A:TYR102 4.3 46.6 1.0
CG A:LYS123 4.3 36.5 1.0
CAF A:5FI402 4.3 44.5 1.0
O A:LYS104 4.4 39.4 1.0
CA A:LYS104 4.4 39.9 1.0
CB A:TYR102 4.5 45.4 1.0
CG A:LEU125 4.5 42.2 1.0
C A:LYS104 4.5 34.7 1.0
CAX A:5FI402 4.5 41.2 1.0
CA A:TYR102 4.7 43.1 1.0
CD A:LYS123 4.7 35.0 1.0
C A:VAL124 4.8 44.6 1.0
CAY A:5FI402 4.9 40.3 1.0
CA A:LEU125 4.9 38.7 1.0
N A:TYR102 5.0 43.1 1.0

Fluorine binding site 2 out of 3 in 3we4

Go back to Fluorine Binding Sites List in 3we4
Fluorine binding site 2 out of 3 in the Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole


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 S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:51.1
occ:1.00
 FAC A:5FI402 0.0 51.1 1.0
CBB A:5FI402 1.3 47.5 1.0
FAD A:5FI402 2.1 48.5 1.0
FAB A:5FI402 2.1 50.6 1.0
CAU A:5FI402 2.4 41.2 1.0
CAE A:5FI402 2.8 35.9 1.0
N A:GLY103 3.4 44.5 1.0
CAI A:5FI402 3.5 39.6 1.0
CB A:TYR102 3.5 45.4 1.0
N A:TYR102 3.6 43.1 1.0
C A:TYR102 3.7 45.0 1.0
CA A:TYR102 3.8 43.1 1.0
O A:GLY103 3.9 42.5 1.0
O A:CYS240 4.0 74.6 1.0
C A:GLY103 4.1 41.8 1.0
CA A:GLY103 4.1 38.0 1.0
CAF A:5FI402 4.1 44.5 1.0
CA A:GLY100 4.2 44.6 1.0
C A:GLY100 4.3 49.0 1.0
CA A:LYS241 4.3 59.5 1.0
CD2 A:LEU125 4.4 50.5 1.0
N A:GLY101 4.5 49.1 1.0
O A:TYR102 4.5 46.6 1.0
CD2 A:TYR102 4.5 53.4 1.0
CG A:TYR102 4.5 51.5 1.0
N A:GLY100 4.6 43.8 1.0
CAX A:5FI402 4.6 41.2 1.0
O A:GLY100 4.7 50.8 1.0
C A:GLY101 4.7 49.2 1.0
C A:CYS240 4.8 73.6 1.0
N A:LYS104 4.9 35.3 1.0
CAY A:5FI402 4.9 40.3 1.0
CB A:LYS241 4.9 49.4 1.0
C A:LYS241 4.9 74.2 1.0

Fluorine binding site 3 out of 3 in 3we4

Go back to Fluorine Binding Sites List in 3we4
Fluorine binding site 3 out of 3 in the Crystal Structure of S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole


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 S6K1 Kinase Domain in Complex with A Pyrimidine Derivative Pf-4708671 2-{[4-(5-Ethylpyrimidin-4-Yl)Piperazin-1- Yl]Methyl}-5-(Trifluoromethyl)-1H-Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:48.5
occ:1.00
 FAD A:5FI402 0.0 48.5 1.0
CBB A:5FI402 1.3 47.5 1.0
FAC A:5FI402 2.1 51.1 1.0
FAB A:5FI402 2.1 50.6 1.0
CAU A:5FI402 2.4 41.2 1.0
CAI A:5FI402 2.8 39.6 1.0
O A:HOH681 3.3 51.3 1.0
CE A:LYS123 3.3 51.0 1.0
CD2 A:LEU125 3.4 50.5 1.0
CAE A:5FI402 3.7 35.9 1.0
O A:LEU239 4.0 50.2 1.0
NZ A:LYS123 4.0 58.4 1.0
CB A:LEU239 4.2 51.2 1.0
CAX A:5FI402 4.2 41.2 1.0
O A:HOH566 4.2 59.2 1.0
CB A:TYR102 4.3 45.4 1.0
O A:CYS240 4.3 74.6 1.0
C A:LEU239 4.5 65.6 1.0
CD A:LYS123 4.6 35.0 1.0
CA A:LYS241 4.8 59.5 1.0
CA A:LEU239 4.8 48.7 1.0
CAF A:5FI402 4.8 44.5 1.0
CG A:LYS123 4.9 36.5 1.0
CG A:LEU125 4.9 42.2 1.0
C A:CYS240 4.9 73.6 1.0
N A:LEU239 4.9 48.8 1.0
N A:GLY103 4.9 44.5 1.0
C A:TYR102 4.9 45.0 1.0

Reference:

H.Niwa, J.Mikuni, S.Sasaki, Y.Tomabechi, K.Honda, M.Ikeda, N.Ohsawa, M.Wakiyama, N.Handa, M.Shirouzu, T.Honma, A.Tanaka, S.Yokoyama. Crystal Structures of the S6K1 Kinase Domain in Complexes with Inhibitors J.Struct.Funct.Genom. V. 15 153 2014.
ISSN: ISSN 1345-711X
PubMed: 25078151
DOI: 10.1007/S10969-014-9188-8
Page generated: Mon Jul 14 20:04:36 2025

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