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Fluorine in PDB 3wf7: Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide

Enzymatic activity of Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide

All present enzymatic activity of Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide, PDB code: 3wf7 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) 49.10 / 1.85
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.438, 69.438, 145.649, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.4

Other elements in 3wf7:

The structure of Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide 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 Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide (pdb code 3wf7). 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 Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide, PDB code: 3wf7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3wf7

Go back to Fluorine Binding Sites List in 3wf7
Fluorine binding site 1 out of 3 in the Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide


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 Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:75.4
occ:1.00
 F16 A:FS9402 0.0 75.4 1.0
C15 A:FS9402 1.3 66.9 1.0
F18 A:FS9402 2.1 69.1 1.0
F17 A:FS9402 2.1 75.2 1.0
C14 A:FS9402 2.4 52.2 1.0
C13 A:FS9402 3.0 52.8 1.0
N A:LYS104 3.2 32.4 1.0
CD2 A:LEU125 3.2 57.0 1.0
C19 A:FS9402 3.4 48.7 1.0
C A:GLY103 3.6 34.0 1.0
O A:LYS104 3.6 34.5 1.0
CG2 A:VAL105 3.6 31.6 1.0
C A:LYS104 3.6 33.9 1.0
CA A:LYS104 3.8 33.3 1.0
CA A:GLY103 4.0 37.5 1.0
O A:GLY103 4.1 41.5 1.0
N A:VAL105 4.3 27.0 1.0
C12 A:FS9402 4.3 49.8 1.0
CB A:LYS123 4.3 35.6 1.0
O A:VAL124 4.4 39.4 1.0
N A:GLY103 4.4 43.0 1.0
C20 A:FS9402 4.5 49.7 1.0
N A:VAL124 4.6 27.9 1.0
CD A:LYS123 4.7 33.9 1.0
CG A:LEU125 4.7 52.8 1.0
CA A:LYS123 4.8 29.1 1.0
CG A:LYS123 4.8 28.4 1.0
C A:VAL124 4.8 42.3 1.0
CB A:VAL105 4.9 31.2 1.0
CA A:VAL105 4.9 26.8 1.0
C21 A:FS9402 4.9 51.6 1.0
O10 A:FS9402 4.9 45.5 1.0

Fluorine binding site 2 out of 3 in 3wf7

Go back to Fluorine Binding Sites List in 3wf7
Fluorine binding site 2 out of 3 in the Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide


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 Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:75.2
occ:1.00
 F17 A:FS9402 0.0 75.2 1.0
C15 A:FS9402 1.3 66.9 1.0
F16 A:FS9402 2.1 75.4 1.0
F18 A:FS9402 2.1 69.1 1.0
C14 A:FS9402 2.4 52.2 1.0
C19 A:FS9402 2.8 48.7 1.0
N A:GLY103 3.1 43.0 1.0
CB A:TYR102 3.3 58.7 1.0
CD2 A:LEU125 3.3 57.0 1.0
CA A:GLY103 3.4 37.5 1.0
C A:TYR102 3.5 52.7 1.0
C A:GLY103 3.5 34.0 1.0
C13 A:FS9402 3.6 52.8 1.0
O A:GLY103 3.8 41.5 1.0
N A:LYS104 3.9 32.4 1.0
CA A:TYR102 3.9 55.2 1.0
O A:TYR102 4.1 46.6 1.0
C20 A:FS9402 4.1 49.7 1.0
N A:TYR102 4.3 48.2 1.0
CG A:TYR102 4.6 60.1 1.0
CG A:LEU125 4.8 52.8 1.0
CD A:LYS241 4.8 64.8 1.0
C12 A:FS9402 4.8 49.8 1.0
CA A:LYS104 4.9 33.3 1.0
O A:VAL124 4.9 39.4 1.0
C21 A:FS9402 5.0 51.6 1.0
CD2 A:TYR102 5.0 67.2 1.0

Fluorine binding site 3 out of 3 in 3wf7

Go back to Fluorine Binding Sites List in 3wf7
Fluorine binding site 3 out of 3 in the Crystal Structure of S6K1 Kinase Domain in Complex with A Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide


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 Purine Derivative 1-(9H-Purin-6-Yl)-N-[3-(Trifluoromethyl)Phenyl]Piperidine- 4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:69.1
occ:1.00
 F18 A:FS9402 0.0 69.1 1.0
C15 A:FS9402 1.3 66.9 1.0
F16 A:FS9402 2.1 75.4 1.0
F17 A:FS9402 2.1 75.2 1.0
C14 A:FS9402 2.4 52.2 1.0
C13 A:FS9402 2.9 52.8 1.0
CD A:LYS241 3.2 64.8 1.0
CD2 A:LEU125 3.2 57.0 1.0
C19 A:FS9402 3.5 48.7 1.0
CE A:LYS241 3.5 66.7 1.0
C12 A:FS9402 4.2 49.8 1.0
CD A:LYS123 4.4 33.9 1.0
O10 A:FS9402 4.5 45.5 1.0
CG A:LYS241 4.5 67.7 1.0
CG A:LEU125 4.5 52.8 1.0
C20 A:FS9402 4.6 49.7 1.0
CG2 A:VAL105 4.7 31.6 1.0
CB A:TYR102 4.7 58.7 1.0
CD1 A:LEU125 4.9 62.6 1.0
CB A:LYS241 4.9 65.0 1.0
NZ A:LYS241 4.9 55.7 1.0
C21 A:FS9402 4.9 51.6 1.0
CB A:LYS123 4.9 35.6 1.0
CA A:LYS241 5.0 69.7 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 23:31:41 2024

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