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Fluorine in PDB 4kbi: Hcv NS5B GT1B N316Y with Cmpd 4

Enzymatic activity of Hcv NS5B GT1B N316Y with Cmpd 4

All present enzymatic activity of Hcv NS5B GT1B N316Y with Cmpd 4:
2.7.7.48;

Protein crystallography data

The structure of Hcv NS5B GT1B N316Y with Cmpd 4, PDB code: 4kbi was solved by S.P.Williams, K.M.Kahler, J.B.Shotwell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.72 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.040, 106.450, 126.490, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 25

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hcv NS5B GT1B N316Y with Cmpd 4 (pdb code 4kbi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Hcv NS5B GT1B N316Y with Cmpd 4, PDB code: 4kbi:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 4kbi

Go back to Fluorine Binding Sites List in 4kbi
Fluorine binding site 1 out of 4 in the Hcv NS5B GT1B N316Y with Cmpd 4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hcv NS5B GT1B N316Y with Cmpd 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:26.3
occ:1.00
F22 A:1C0601 0.0 26.3 1.0
C21 A:1C0601 1.3 26.2 1.0
C23 A:1C0601 2.4 25.1 1.0
C20 A:1C0601 2.4 27.4 1.0
B18 A:1C0601 3.2 28.4 1.0
O19 A:1C0601 3.4 30.1 1.0
C15 A:1C0601 3.6 27.3 1.0
C13 A:1C0601 3.6 23.9 1.0
C14 A:1C0601 4.1 25.9 1.0
C32 A:1C0601 4.1 17.4 1.0
CE2 A:TYR316 4.4 20.1 1.0
O17 A:1C0601 4.5 29.0 1.0
CB A:CYS366 4.5 20.2 1.0
C16 A:1C0601 4.7 28.0 1.0
C12 A:1C0601 4.9 21.4 1.0
O A:CYS366 4.9 20.2 1.0
C31 A:1C0601 4.9 17.3 1.0
SG A:CYS366 5.0 22.7 1.0

Fluorine binding site 2 out of 4 in 4kbi

Go back to Fluorine Binding Sites List in 4kbi
Fluorine binding site 2 out of 4 in the Hcv NS5B GT1B N316Y with Cmpd 4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hcv NS5B GT1B N316Y with Cmpd 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:17.6
occ:1.00
F38 A:1C0601 0.0 17.6 1.0
C37 A:1C0601 1.3 17.8 1.0
C36 A:1C0601 2.3 17.6 1.0
C39 A:1C0601 2.3 18.1 1.0
CG2 A:ILE363 3.1 20.9 1.0
CB A:ILE363 3.3 21.7 1.0
C35 A:1C0601 3.6 17.7 1.0
C40 A:1C0601 3.6 18.0 1.0
O A:HOH705 3.9 4.8 1.0
CD1 A:LEU360 3.9 22.9 1.0
CD1 A:ILE363 4.0 21.7 1.0
CG1 A:VAL321 4.0 14.7 1.0
O A:ILE363 4.1 21.3 1.0
C34 A:1C0601 4.1 18.0 1.0
CG1 A:ILE363 4.2 22.6 1.0
CG2 A:VAL321 4.3 13.6 1.0
O A:LEU360 4.4 23.4 1.0
C A:ILE363 4.5 21.5 1.0
CD2 A:LEU204 4.5 20.0 1.0
CA A:ILE363 4.5 22.0 1.0
CB A:VAL321 4.7 14.2 1.0
CD1 A:LEU204 4.8 19.1 1.0

Fluorine binding site 3 out of 4 in 4kbi

Go back to Fluorine Binding Sites List in 4kbi
Fluorine binding site 3 out of 4 in the Hcv NS5B GT1B N316Y with Cmpd 4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hcv NS5B GT1B N316Y with Cmpd 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:26.7
occ:1.00
F22 B:1C0601 0.0 26.7 1.0
C21 B:1C0601 1.3 26.1 1.0
C23 B:1C0601 2.4 25.4 1.0
C20 B:1C0601 2.4 27.4 1.0
B18 B:1C0601 3.2 28.0 1.0
O19 B:1C0601 3.4 29.3 1.0
O B:HOH1041 3.5 28.0 1.0
C15 B:1C0601 3.5 27.4 1.0
C13 B:1C0601 3.6 24.1 1.0
C14 B:1C0601 4.0 26.2 1.0
C32 B:1C0601 4.1 19.4 1.0
CE2 B:TYR316 4.3 21.4 1.0
O17 B:1C0601 4.5 29.1 1.0
CB B:CYS366 4.5 20.1 1.0
C16 B:1C0601 4.7 28.1 1.0
O B:CYS366 4.8 19.9 1.0
C31 B:1C0601 4.9 19.5 1.0
SG B:CYS366 4.9 20.8 1.0
C12 B:1C0601 4.9 22.3 1.0
CD2 B:TYR316 4.9 20.5 1.0

Fluorine binding site 4 out of 4 in 4kbi

Go back to Fluorine Binding Sites List in 4kbi
Fluorine binding site 4 out of 4 in the Hcv NS5B GT1B N316Y with Cmpd 4


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hcv NS5B GT1B N316Y with Cmpd 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:21.6
occ:1.00
F38 B:1C0601 0.0 21.6 1.0
C37 B:1C0601 1.3 20.1 1.0
C36 B:1C0601 2.3 19.8 1.0
C39 B:1C0601 2.4 20.3 1.0
CG2 B:ILE363 3.2 22.6 1.0
CB B:ILE363 3.3 23.2 1.0
C35 B:1C0601 3.6 19.4 1.0
C40 B:1C0601 3.6 19.4 1.0
O B:HOH701 3.8 6.3 1.0
CD1 B:ILE363 3.8 23.0 1.0
CD1 B:LEU360 3.9 23.1 1.0
C34 B:1C0601 4.1 18.9 1.0
CG1 B:VAL321 4.1 14.5 1.0
CG1 B:ILE363 4.2 23.9 1.0
O B:ILE363 4.3 22.7 1.0
CG2 B:VAL321 4.3 13.4 1.0
O B:LEU360 4.4 23.1 1.0
CD1 B:LEU204 4.4 20.8 1.0
C B:ILE363 4.6 22.8 1.0
CA B:ILE363 4.6 23.4 1.0
CD2 B:LEU204 4.6 20.9 1.0
CB B:VAL321 4.8 14.2 1.0

Reference:

A.Maynard, R.M.Crosby, B.Ellis, R.Hamatake, Z.Hong, B.A.Johns, K.M.Kahler, C.Koble, A.Leivers, M.R.Leivers, A.Mathis, A.J.Peat, J.J.Pouliot, C.D.Roberts, V.Samano, R.M.Schmidt, G.K.Smith, A.Spaltenstein, E.L.Stewart, P.Thommes, E.M.Turner, C.Voitenleitner, J.T.Walker, G.Waitt, J.Weatherhead, K.Weaver, S.Williams, L.Wright, Z.Z.Xiong, D.Haigh, J.B.Shotwell. Discovery of A Potent Boronic Acid Derived Inhibitor of the Hcv Rna-Dependent Rna Polymerase. J.Med.Chem. V. 57 1902 2014.
ISSN: ISSN 0022-2623
PubMed: 23672667
DOI: 10.1021/JM400317W
Page generated: Mon Jul 14 22:49:59 2025

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