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Zinc 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:

Fluorine (F) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 in 3we4

Go back to Zinc Binding Sites List in 3we4
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn401

b:72.1
occ:1.00
 ND1 A:HIS251 2.1 55.5 1.0
ND1 A:HIS245 2.3 85.8 1.0
SG A:CYS254 2.3 67.8 1.0
SG A:CYS240 2.4 68.2 1.0
CE1 A:HIS251 2.9 67.2 1.0
CB A:CYS254 3.1 60.8 1.0
CB A:CYS240 3.2 55.4 1.0
CG A:HIS251 3.2 55.6 1.0
CG A:HIS245 3.2 96.3 1.0
CE1 A:HIS245 3.3 90.5 1.0
CB A:HIS245 3.4 0.8 1.0
CB A:HIS251 3.6 63.8 1.0
CA A:HIS245 3.9 0.7 1.0
NE2 A:HIS251 4.1 56.7 1.0
CA A:HIS251 4.1 69.7 1.0
CD2 A:HIS251 4.2 47.8 1.0
CD2 A:HIS245 4.4 97.1 1.0
NE2 A:HIS245 4.4 100.0 1.0
O A:ILE244 4.6 0.3 1.0
CA A:CYS254 4.6 65.1 1.0
CB A:GLU242 4.6 71.2 1.0
CA A:CYS240 4.7 72.2 1.0
O A:HIS251 4.7 66.5 1.0
N A:ASP246 4.8 0.3 1.0
O A:THR250 4.8 0.1 1.0
N A:HIS245 4.8 0.6 1.0
C A:HIS245 4.9 0.7 1.0
CG A:GLU242 4.9 66.7 1.0
C A:HIS251 4.9 67.0 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 Dec 16 04:57:16 2020

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