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Fluorine in PDB 4kai: Hcv NS5B GT1B N316 with GSK5852A

Enzymatic activity of Hcv NS5B GT1B N316 with GSK5852A

All present enzymatic activity of Hcv NS5B GT1B N316 with GSK5852A:
2.7.7.48;

Protein crystallography data

The structure of Hcv NS5B GT1B N316 with GSK5852A, PDB code: 4kai 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) 81.86 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.708, 107.451, 126.382, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 24

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hcv NS5B GT1B N316 with GSK5852A (pdb code 4kai). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Hcv NS5B GT1B N316 with GSK5852A, PDB code: 4kai:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 1 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


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 N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:23.3
occ:1.00
 F37 A:1PV601 0.0 23.3 1.0
C36 A:1PV601 1.3 21.6 1.0
C35 A:1PV601 2.4 21.1 1.0
C38 A:1PV601 2.4 21.4 1.0
CG2 A:ILE363 3.0 22.0 1.0
CB A:ILE363 3.2 23.0 1.0
C34 A:1PV601 3.6 20.5 1.0
C39 A:1PV601 3.7 20.5 1.0
CD1 A:LEU360 3.7 25.0 1.0
O A:HOH748 3.8 17.3 1.0
CD1 A:ILE363 3.9 22.8 1.0
O A:ILE363 4.0 22.4 1.0
O A:LEU360 4.0 26.8 1.0
CG1 A:ILE363 4.1 23.6 1.0
C33 A:1PV601 4.1 20.2 1.0
C A:ILE363 4.3 22.5 1.0
CA A:ILE363 4.3 23.4 1.0
CG1 A:VAL321 4.5 17.8 1.0
CG2 A:VAL321 4.5 16.8 1.0
CD2 A:LEU204 4.7 19.0 1.0
CD1 A:LEU204 4.7 18.8 1.0
CG A:LEU360 4.8 27.1 1.0
CG2 A:VAL370 4.9 23.3 1.0

Fluorine binding site 2 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 2 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


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 N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F601

b:27.0
occ:1.00
 F21 A:1PV601 0.0 27.0 1.0
C20 A:1PV601 1.4 25.8 1.0
C22 A:1PV601 2.4 25.3 1.0
C16 A:1PV601 2.4 25.7 1.0
O19 A:1PV601 2.6 28.2 1.0
B17 A:1PV601 2.9 26.5 1.0
SD A:MET414 3.1 16.6 0.5
O A:HOH793 3.1 13.6 1.0
N A:TYR448 3.3 22.4 1.0
C13 A:1PV601 3.6 24.0 1.0
CD1 A:TYR448 3.6 23.5 1.0
C15 A:1PV601 3.7 24.7 1.0
CA A:TYR448 3.8 22.3 1.0
CE A:MET414 3.9 16.1 0.5
C14 A:1PV601 4.1 24.9 1.0
O18 A:1PV601 4.3 26.1 1.0
CE1 A:TYR448 4.3 24.4 1.0
O A:HOH970 4.4 17.1 1.0
C A:ILE447 4.4 22.8 1.0
CA A:ILE447 4.6 23.2 1.0
CG A:TYR448 4.7 23.0 1.0
C32 A:1PV601 4.7 18.5 1.0
CG A:MET414 4.7 14.9 0.5
CG A:MET414 4.8 15.4 0.5
C30 A:1PV601 4.8 19.1 1.0
N A:GLY449 4.8 22.0 1.0
CB A:TYR448 4.8 22.3 1.0
C A:TYR448 4.8 22.1 1.0
C12 A:1PV601 4.8 23.2 1.0
SD A:MET414 4.9 18.8 0.5
O A:GLN446 4.9 24.1 1.0
C24 A:1PV601 5.0 20.9 1.0

Fluorine binding site 3 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 3 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


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 N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:54.7
occ:1.00
 F37 A:1PV602 0.0 54.7 1.0
C36 A:1PV602 1.4 53.3 1.0
C35 A:1PV602 2.4 52.9 1.0
C38 A:1PV602 2.4 52.7 1.0
C34 A:1PV602 3.7 52.0 1.0
C39 A:1PV602 3.7 51.9 1.0
C33 A:1PV602 4.2 50.7 1.0

Fluorine binding site 4 out of 8 in 4kai

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Fluorine binding site 4 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


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 N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:39.4
occ:1.00
 F21 A:1PV602 0.0 39.4 1.0
C20 A:1PV602 1.3 37.3 1.0
C16 A:1PV602 2.4 36.5 1.0
C22 A:1PV602 2.4 37.5 1.0
O19 A:1PV602 2.7 35.8 1.0
B17 A:1PV602 2.8 35.7 1.0
C15 A:1PV602 3.6 36.4 1.0
C13 A:1PV602 3.7 37.7 1.0
O18 A:1PV602 3.7 34.4 1.0
CG2 A:ILE482 4.1 23.6 1.0
C14 A:1PV602 4.1 37.1 1.0
CD1 A:LEU497 4.8 22.1 1.0
C12 A:1PV602 4.9 38.3 1.0

Fluorine binding site 5 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 5 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hcv NS5B GT1B N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:23.8
occ:1.00
 F37 B:1PV601 0.0 23.8 1.0
C36 B:1PV601 1.3 21.4 1.0
C38 B:1PV601 2.4 20.5 1.0
C35 B:1PV601 2.4 21.0 1.0
CG2 B:ILE363 3.1 21.7 1.0
CB B:ILE363 3.2 22.3 1.0
C34 B:1PV601 3.6 20.7 1.0
C39 B:1PV601 3.6 19.9 1.0
O B:HOH711 3.7 9.4 1.0
CD1 B:LEU360 3.8 23.0 1.0
CD1 B:ILE363 3.8 21.8 1.0
O B:ILE363 4.0 21.3 1.0
CG1 B:ILE363 4.1 23.1 1.0
O B:LEU360 4.1 24.7 1.0
C33 B:1PV601 4.1 19.9 1.0
C B:ILE363 4.3 21.9 1.0
CA B:ILE363 4.3 22.8 1.0
CG1 B:VAL321 4.4 15.7 1.0
CD2 B:LEU204 4.5 19.7 1.0
CG2 B:VAL321 4.6 15.1 1.0
CD1 B:LEU204 4.6 19.7 1.0

Fluorine binding site 6 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 6 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hcv NS5B GT1B N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F601

b:23.9
occ:1.00
 F21 B:1PV601 0.0 23.9 1.0
C20 B:1PV601 1.4 23.6 1.0
C22 B:1PV601 2.4 23.0 1.0
C16 B:1PV601 2.4 23.4 1.0
O19 B:1PV601 2.8 25.2 1.0
B17 B:1PV601 2.9 24.7 1.0
O B:HOH779 2.9 19.3 1.0
N B:TYR448 3.1 20.4 1.0
O B:HOH965 3.2 29.1 1.0
SD B:MET414 3.3 15.3 0.5
CA B:TYR448 3.6 19.9 1.0
CD1 B:TYR448 3.6 19.7 1.0
C13 B:1PV601 3.7 22.1 1.0
C15 B:1PV601 3.7 22.4 1.0
CE B:MET414 3.8 15.2 0.5
C B:ILE447 4.2 21.0 1.0
C14 B:1PV601 4.2 22.3 1.0
O18 B:1PV601 4.2 24.6 1.0
CE1 B:TYR448 4.3 20.4 1.0
CA B:ILE447 4.4 21.7 1.0
CG B:TYR448 4.6 20.1 1.0
N B:GLY449 4.6 19.6 1.0
C32 B:1PV601 4.6 17.9 1.0
C B:TYR448 4.6 19.6 1.0
CB B:TYR448 4.7 19.9 1.0
O B:HOH966 4.7 16.7 1.0
O B:GLN446 4.7 22.8 1.0
C30 B:1PV601 4.7 18.8 1.0
C12 B:1PV601 4.9 21.6 1.0
CG B:MET414 4.9 14.6 0.5
O B:HOH955 5.0 23.3 1.0

Fluorine binding site 7 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 7 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Hcv NS5B GT1B N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:57.2
occ:1.00
 F37 B:1PV602 0.0 57.2 1.0
C36 B:1PV602 1.4 56.1 1.0
C38 B:1PV602 2.4 55.8 1.0
C35 B:1PV602 2.4 55.7 1.0
C34 B:1PV602 3.7 55.3 1.0
C39 B:1PV602 3.7 55.2 1.0
C33 B:1PV602 4.2 54.5 1.0

Fluorine binding site 8 out of 8 in 4kai

Go back to Fluorine Binding Sites List in 4kai
Fluorine binding site 8 out of 8 in the Hcv NS5B GT1B N316 with GSK5852A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Hcv NS5B GT1B N316 with GSK5852A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:42.4
occ:1.00
 F21 B:1PV602 0.0 42.4 1.0
C20 B:1PV602 1.3 42.5 1.0
C22 B:1PV602 2.4 42.9 1.0
C16 B:1PV602 2.4 42.5 1.0
B17 B:1PV602 2.9 42.1 1.0
O18 B:1PV602 3.2 41.2 1.0
CB B:LEU497 3.6 24.4 1.0
C13 B:1PV602 3.7 43.3 1.0
C15 B:1PV602 3.7 42.5 1.0
N B:ARG498 3.7 26.7 1.0
C B:LEU497 3.8 25.5 1.0
O B:HOH841 4.0 15.7 1.0
O B:LEU497 4.0 25.3 1.0
CA B:ARG498 4.0 27.9 1.0
O B:HOH967 4.1 19.0 1.0
O19 B:1PV602 4.1 41.7 1.0
C14 B:1PV602 4.2 42.9 1.0
CE B:MET423 4.2 19.1 1.0
CA B:LEU497 4.3 24.7 1.0
CB B:ARG498 4.5 29.2 1.0
C9 B:1PV602 4.6 48.2 1.0
CD1 B:LEU497 4.7 23.9 1.0
CG B:LEU497 4.8 23.8 1.0
C8 B:1PV602 4.8 50.0 1.0
SD B:MET423 4.9 19.7 1.0
C12 B:1PV602 4.9 43.9 1.0
O7 B:1PV602 5.0 51.6 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: Thu Aug 1 03:08:36 2024

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