Atomistry » Fluorine » PDB 3vrs-3wyk » 3we4
Atomistry »
  Fluorine »
    PDB 3vrs-3wyk »
      3we4 »

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: Wed Jul 31 23:31:25 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy