Fluorine in PDB 2jc0: Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264

The structure of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264, PDB code: 2jc0 was solved by A.Wonacott, T.Skarzynski, O.M.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.2
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	85.740, 105.893, 126.120, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 (pdb code 2jc0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264, PDB code: 2jc0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


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 Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1563 b:39.4 occ:1.00 F54 A:6991563 0.0 39.4 1.0 C51 A:6991563 1.4 37.2 1.0 F52 A:6991563 2.2 39.6 1.0 F53 A:6991563 2.3 36.4 1.0 C2 A:6991563 2.4 38.3 1.0 C1 A:6991563 3.1 37.2 1.0 CB A:CYS366 3.2 31.9 1.0 OG A:SER368 3.3 28.5 1.0 CD2 A:LEU384 3.3 28.2 1.0 C3 A:6991563 3.4 35.4 1.0 CB A:SER368 3.5 29.6 1.0 NE A:ARG200 3.6 24.2 1.0 CD A:ARG200 3.8 26.1 1.0 O A:CYS366 3.8 32.5 1.0 O A:SER365 3.9 31.1 1.0 O A:HOH2234 3.9 28.6 1.0 CZ A:ARG200 4.2 27.5 1.0 SG A:CYS366 4.3 32.6 1.0 C6 A:6991563 4.4 35.5 1.0 CA A:CYS366 4.4 32.9 1.0 OH A:TYR415 4.4 24.2 1.0 CG A:LEU384 4.4 27.8 1.0 C A:CYS366 4.5 32.6 1.0 CD1 A:LEU384 4.6 26.8 1.0 C4 A:6991563 4.6 35.6 1.0 NH2 A:ARG200 4.6 22.5 1.0 NH1 A:ARG200 4.8 24.1 1.0 C A:SER365 4.8 31.8 1.0 CA A:SER368 4.9 29.5 1.0

Fluorine binding site 2 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


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 Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1563 b:39.6 occ:1.00 F52 A:6991563 0.0 39.6 1.0 C51 A:6991563 1.3 37.2 1.0 F53 A:6991563 2.2 36.4 1.0 F54 A:6991563 2.2 39.4 1.0 C2 A:6991563 2.2 38.3 1.0 C1 A:6991563 2.8 37.2 1.0 CD A:ARG200 3.2 26.1 1.0 CD2 A:LEU384 3.2 28.2 1.0 C3 A:6991563 3.4 35.4 1.0 OH A:TYR448 3.9 29.0 1.0 NE A:ARG200 3.9 24.2 1.0 O A:HOH2145 4.0 30.5 1.0 C6 A:6991563 4.1 35.5 1.0 CE1 A:TYR448 4.4 30.6 1.0 C4 A:6991563 4.5 35.6 1.0 CG A:PRO197 4.5 28.7 1.0 CA A:PRO197 4.5 28.0 1.0 CZ A:ARG200 4.6 27.5 1.0 CG A:ARG200 4.6 25.4 1.0 CB A:PRO197 4.6 28.1 1.0 CZ A:TYR448 4.6 30.0 1.0 CG A:LEU384 4.7 27.8 1.0 NH1 A:ARG200 4.7 24.1 1.0 CB A:ARG200 4.8 26.0 1.0 C5 A:6991563 4.8 36.0 1.0 CE A:MET414 4.9 29.6 1.0 OG A:SER368 5.0 28.5 1.0

Fluorine binding site 3 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


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 Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1563 b:36.4 occ:1.00 F53 A:6991563 0.0 36.4 1.0 C51 A:6991563 1.3 37.2 1.0 F52 A:6991563 2.2 39.6 1.0 C2 A:6991563 2.3 38.3 1.0 F54 A:6991563 2.3 39.4 1.0 C3 A:6991563 2.6 35.4 1.0 O A:HOH2145 3.2 30.5 1.0 NH1 A:ARG200 3.2 24.1 1.0 CZ A:ARG200 3.3 27.5 1.0 NE A:ARG200 3.3 24.2 1.0 CD A:ARG200 3.4 26.1 1.0 SG A:CYS366 3.5 32.6 1.0 CB A:CYS366 3.5 31.9 1.0 C1 A:6991563 3.6 37.2 1.0 ND2 A:ASN316 3.8 29.6 1.0 C4 A:6991563 4.0 35.6 1.0 NH2 A:ARG200 4.1 22.5 1.0 OH A:TYR448 4.3 29.0 1.0 CG A:ASN316 4.4 25.1 1.0 CE1 A:TYR448 4.5 30.6 1.0 OD1 A:ASN316 4.6 27.5 1.0 C6 A:6991563 4.7 35.5 1.0 CZ A:TYR448 4.8 30.0 1.0 CG A:ARG200 4.8 25.4 1.0 C5 A:6991563 4.9 36.0 1.0 CD2 A:LEU384 5.0 28.2 1.0

Fluorine binding site 4 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1564 b:37.0 occ:0.50 F54 A:6991564 0.0 37.0 0.5 C51 A:6991564 1.3 36.7 0.5 F52 A:6991564 2.2 36.5 0.5 F53 A:6991564 2.2 38.9 0.5 C2 A:6991564 2.3 36.5 0.5 CG A:MET423 2.5 28.8 1.0 CD2 A:TRP528 2.8 26.1 1.0 C1 A:6991564 2.8 36.9 0.5 CE3 A:TRP528 3.0 27.7 1.0 CE2 A:TRP528 3.2 24.7 1.0 SD A:MET423 3.3 34.7 1.0 CG A:TRP528 3.4 28.4 1.0 CZ3 A:TRP528 3.4 26.0 1.0 C3 A:6991564 3.6 35.8 0.5 CZ2 A:TRP528 3.6 24.2 1.0 CH2 A:TRP528 3.7 26.7 1.0 NE1 A:TRP528 3.8 24.7 1.0 CB A:MET423 3.8 26.0 1.0 CD1 A:TRP528 3.9 25.3 1.0 N A:MET423 3.9 25.4 1.0 CB A:ARG422 4.0 23.6 1.0 CA A:MET423 4.0 26.5 1.0 CB A:TRP528 4.1 29.8 1.0 CE A:MET423 4.2 31.3 1.0 C6 A:6991564 4.2 36.3 0.5 C A:ARG422 4.4 24.9 1.0 O A:LEU419 4.6 22.9 1.0 C4 A:6991564 4.7 36.0 0.5 NH1 A:ARG422 4.8 28.2 1.0 CA A:ARG422 4.8 24.5 1.0 CZ A:ARG422 4.8 29.8 1.0 NE A:ARG422 4.9 26.3 1.0

Fluorine binding site 5 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1564 b:36.5 occ:0.50 F52 A:6991564 0.0 36.5 0.5 C51 A:6991564 1.4 36.7 0.5 F54 A:6991564 2.2 37.0 0.5 F53 A:6991564 2.2 38.9 0.5 C2 A:6991564 2.4 36.5 0.5 C1 A:6991564 3.2 36.9 0.5 C3 A:6991564 3.2 35.8 0.5 CB A:ARG422 3.3 23.6 1.0 CA A:LEU419 3.4 24.8 1.0 CG A:MET423 3.4 28.8 1.0 O A:LEU419 3.5 22.9 1.0 NH1 A:ARG422 3.7 28.2 1.0 CD A:ARG422 3.8 25.7 1.0 C A:LEU419 3.8 24.0 1.0 OH A:TYR477 3.9 25.0 1.0 SD A:MET423 3.9 34.7 1.0 CG A:ARG422 4.1 22.6 1.0 N A:MET423 4.1 25.4 1.0 O A:THR418 4.1 24.1 1.0 CE1 A:TYR477 4.1 28.8 1.0 CB A:LEU419 4.1 24.8 1.0 NE A:ARG422 4.1 26.3 1.0 CZ A:ARG422 4.2 29.8 1.0 CD1 A:LEU419 4.2 30.2 1.0 N A:LEU419 4.3 24.8 1.0 CZ A:TYR477 4.4 27.4 1.0 CA A:ARG422 4.4 24.5 1.0 C4 A:6991564 4.5 36.0 0.5 CB A:MET423 4.5 26.0 1.0 C6 A:6991564 4.5 36.3 0.5 C A:THR418 4.5 24.6 1.0 C A:ARG422 4.6 24.9 1.0 CA A:MET423 4.8 26.5 1.0 CD2 A:TRP528 4.8 26.1 1.0 CG A:LEU419 4.8 30.6 1.0 CG A:TRP528 4.8 28.4 1.0 N A:ARG422 4.9 24.2 1.0 CE2 A:TRP528 5.0 24.7 1.0 C5 A:6991564 5.0 36.9 0.5

Fluorine binding site 6 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ A:F1564 b:38.9 occ:0.50 F53 A:6991564 0.0 38.9 0.5 C51 A:6991564 1.3 36.7 0.5 F54 A:6991564 2.2 37.0 0.5 F52 A:6991564 2.2 36.5 0.5 C2 A:6991564 2.3 36.5 0.5 C3 A:6991564 2.6 35.8 0.5 NH1 A:ARG422 2.7 28.2 1.0 CZ A:ARG422 2.8 29.8 1.0 CG A:TRP528 3.0 28.4 1.0 CB A:TRP528 3.1 29.8 1.0 NE A:ARG422 3.2 26.3 1.0 NH2 A:ARG422 3.3 31.0 1.0 CD1 A:TRP528 3.3 25.3 1.0 CD2 A:TRP528 3.4 26.1 1.0 C1 A:6991564 3.6 36.9 0.5 CD A:ARG422 3.7 25.7 1.0 CB A:ARG422 3.8 23.6 1.0 NE1 A:TRP528 3.9 24.7 1.0 CE2 A:TRP528 4.0 24.7 1.0 C4 A:6991564 4.0 36.0 0.5 CE3 A:TRP528 4.1 27.7 1.0 O A:HOH2287 4.1 28.8 1.0 CG A:ARG422 4.3 22.6 1.0 O A:LEU474 4.4 32.0 1.0 OH A:TYR477 4.6 25.0 1.0 CG A:MET423 4.6 28.8 1.0 CA A:TRP528 4.7 31.2 1.0 C6 A:6991564 4.7 36.3 0.5 C5 A:6991564 4.9 36.9 0.5 CE1 A:TYR477 5.0 28.8 1.0 CZ2 A:TRP528 5.0 24.2 1.0

Fluorine binding site 7 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1564 b:39.6 occ:1.00 F54 B:6991564 0.0 39.6 1.0 C51 B:6991564 1.4 37.2 1.0 F52 B:6991564 2.2 41.8 1.0 F53 B:6991564 2.3 37.2 1.0 C2 B:6991564 2.4 36.4 1.0 C1 B:6991564 3.1 35.1 1.0 OG B:SER368 3.2 30.9 1.0 CD2 B:LEU384 3.3 26.8 1.0 CB B:CYS366 3.4 29.7 1.0 C3 B:6991564 3.5 35.4 1.0 CB B:SER368 3.5 28.7 1.0 NE B:ARG200 3.6 25.3 1.0 CD B:ARG200 3.8 26.2 1.0 O B:HOH2231 3.8 25.2 1.0 O B:CYS366 3.8 27.4 1.0 O B:SER365 3.9 28.8 1.0 CZ B:ARG200 4.2 28.8 1.0 OH B:TYR415 4.3 25.8 1.0 CG B:LEU384 4.4 26.9 1.0 C6 B:6991564 4.4 34.2 1.0 CD1 B:LEU384 4.5 21.6 1.0 C B:CYS366 4.5 29.2 1.0 SG B:CYS366 4.5 32.0 1.0 CA B:CYS366 4.5 29.8 1.0 NH2 B:ARG200 4.7 27.4 1.0 C4 B:6991564 4.7 36.1 1.0 NH1 B:ARG200 4.8 22.4 1.0 CA B:SER368 4.9 28.7 1.0 C B:SER365 4.9 29.2 1.0

Fluorine binding site 8 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1564 b:41.8 occ:1.00 F52 B:6991564 0.0 41.8 1.0 C51 B:6991564 1.3 37.2 1.0 F53 B:6991564 2.2 37.2 1.0 F54 B:6991564 2.2 39.6 1.0 C2 B:6991564 2.3 36.4 1.0 C1 B:6991564 2.9 35.1 1.0 CD B:ARG200 3.2 26.2 1.0 CD2 B:LEU384 3.3 26.8 1.0 C3 B:6991564 3.4 35.4 1.0 O B:HOH2148 3.8 33.3 1.0 OH B:TYR448 3.8 30.0 1.0 NE B:ARG200 3.9 25.3 1.0 C6 B:6991564 4.2 34.2 1.0 CA B:PRO197 4.4 26.4 1.0 CE1 B:TYR448 4.5 28.6 1.0 CG B:ARG200 4.5 26.1 1.0 C4 B:6991564 4.5 36.1 1.0 CZ B:ARG200 4.6 28.8 1.0 CG B:LEU384 4.6 26.9 1.0 CB B:ARG200 4.6 25.8 1.0 CZ B:TYR448 4.7 30.8 1.0 NH1 B:ARG200 4.7 22.4 1.0 CB B:PRO197 4.7 26.4 1.0 C5 B:6991564 4.9 35.5 1.0 CE B:MET414 4.9 31.7 1.0 CG B:PRO197 4.9 26.6 1.0 CD1 B:LEU384 5.0 21.6 1.0

Fluorine binding site 9 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1564 b:37.2 occ:1.00 F53 B:6991564 0.0 37.2 1.0 C51 B:6991564 1.3 37.2 1.0 F52 B:6991564 2.2 41.8 1.0 C2 B:6991564 2.2 36.4 1.0 F54 B:6991564 2.3 39.6 1.0 C3 B:6991564 2.5 35.4 1.0 O B:HOH2148 3.2 33.3 1.0 NH1 B:ARG200 3.4 22.4 1.0 NE B:ARG200 3.4 25.3 1.0 CD B:ARG200 3.4 26.2 1.0 CZ B:ARG200 3.4 28.8 1.0 CB B:CYS366 3.4 29.7 1.0 SG B:CYS366 3.5 32.0 1.0 C1 B:6991564 3.6 35.1 1.0 ND2 B:ASN316 3.8 26.1 1.0 C4 B:6991564 3.9 36.1 1.0 NH2 B:ARG200 4.2 27.4 1.0 CG B:ASN316 4.4 25.6 1.0 OH B:TYR448 4.4 30.0 1.0 CE1 B:TYR448 4.6 28.6 1.0 OD1 B:ASN316 4.6 28.0 1.0 C6 B:6991564 4.7 34.2 1.0 CG B:ARG200 4.8 26.1 1.0 C5 B:6991564 4.8 35.5 1.0 CZ B:TYR448 4.9 30.8 1.0 CA B:CYS366 5.0 29.8 1.0 CD2 B:LEU384 5.0 26.8 1.0 O B:HOH2231 5.0 25.2 1.0

Fluorine binding site 10 out of 12 in the Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Hepatitis C Virus Polymerase in Complex with Inhibitor SB655264 within 5.0Å range: probe atom residue distance (Å) B Occ B:F1565 b:34.5 occ:0.50 F54 B:6991565 0.0 34.5 0.5 C51 B:6991565 1.4 32.0 0.5 CG B:MET423 2.2 32.8 1.0 F52 B:6991565 2.2 31.2 0.5 F53 B:6991565 2.3 34.0 0.5 C2 B:6991565 2.3 31.7 0.5 C1 B:6991565 2.7 32.0 0.5 SD B:MET423 3.0 39.1 1.0 CE3 B:TRP528 3.1 29.3 1.0 CD2 B:TRP528 3.1 27.2 1.0 CZ3 B:TRP528 3.5 26.0 1.0 CE2 B:TRP528 3.6 26.5 1.0 CB B:MET423 3.6 27.9 1.0 C3 B:6991565 3.6 32.0 0.5 CG B:TRP528 3.7 30.3 1.0 CE B:MET423 3.7 37.1 1.0 CH2 B:TRP528 3.9 28.6 1.0 CZ2 B:TRP528 3.9 25.7 1.0 CA B:MET423 4.0 28.8 1.0 N B:MET423 4.0 25.6 1.0 C6 B:6991565 4.1 31.1 0.5 NE1 B:TRP528 4.2 28.1 1.0 CB B:ARG422 4.3 22.8 1.0 CD1 B:TRP528 4.3 27.7 1.0 CB B:TRP528 4.3 29.4 1.0 O B:LEU419 4.4 27.4 1.0 C B:ARG422 4.6 24.2 1.0 CD1 B:LEU419 4.6 33.1 1.0 C4 B:6991565 4.7 29.6 0.5 C5 B:6991565 4.9 31.0 0.5

M.J.Slater, E.M.Amphlett, D.M.Andrews, G.Bravi, G.Burton, A.G.Cheasty, J.A.Corfield, M.R.Ellis, R.H.Fenwick, S.Fernandes, R.Guidetti, D.Haigh, C.D.Hartley, P.D.Howes, D.L.Jackson, R.L.Jarvest, V.L.Lovegrove, K.J.Medhurst, N.R.Parry, H.Price, P.Shah, O.M.Singh, R.Stocker, P.Thommes, C.Wilkinson, A.Wonacott. Optimization of Novel Acyl Pyrrolidine Inhibitors of Hepatitis C Virus Rna-Dependent Rna Polymerase Leading to A Development Candidate. J.Med.Chem. V. 50 897 2007.
ISSN: ISSN 0022-2623
PubMed: 17269759
DOI: 10.1021/JM061207R