Fluorine in PDB 4ibi: Ebola Virus VP35 Bound to Small Molecule

The structure of Ebola Virus VP35 Bound to Small Molecule, PDB code: 4ibi was solved by C.S.Brown, D.W.Leung, W.Xu, D.M.Borek, Z.Otwinowski, P.Ramanan, A.J.Stubbs, D.S.Peterson, J.M.Binning, G.K.Amarasinghe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.91 / 1.47
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.302, 65.451, 72.653, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.7

The structure of Ebola Virus VP35 Bound to Small Molecule also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Ebola Virus VP35 Bound to Small Molecule (pdb code 4ibi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Ebola Virus VP35 Bound to Small Molecule, PDB code: 4ibi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:24.2 occ:1.00 FAF A:1D8401 0.0 24.2 1.0 CBL A:1D8401 1.3 22.0 1.0 FAG A:1D8401 2.1 22.1 1.0 FAH A:1D8401 2.2 21.0 1.0 CBH A:1D8401 2.3 19.8 1.0 CAO A:1D8401 2.8 20.1 1.0 O A:ASP302 3.4 24.1 1.0 CAR A:1D8401 3.6 18.4 1.0 CE2 A:PHE328 3.6 13.9 1.0 CA A:ILE303 3.7 15.8 1.0 C A:ASP302 3.8 30.4 1.0 CG1 A:ILE303 3.8 19.0 1.0 O A:HOH593 3.9 36.3 1.0 CG2 A:ILE297 3.9 19.8 1.0 N A:ILE303 3.9 18.7 1.0 CZ A:PHE328 4.0 19.4 1.0 CAK A:1D8401 4.1 19.8 1.0 CD A:PRO304 4.3 22.3 1.0 CD2 A:PHE328 4.3 13.7 1.0 CB A:ILE303 4.3 12.9 1.0 CB A:ASP302 4.5 31.2 1.0 CBD A:1D8401 4.7 18.0 1.0 CD1 A:ILE297 4.8 21.6 1.0 CA A:ASP302 4.8 19.6 1.0 C A:ILE303 4.9 16.6 1.0 CAM A:1D8401 4.9 19.1 1.0 CG2 A:ILE303 4.9 18.0 1.0 CB A:ILE297 4.9 18.9 1.0 CE1 A:PHE328 5.0 19.6 1.0

Fluorine binding site 2 out of 6 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:22.1 occ:1.00 FAG A:1D8401 0.0 22.1 1.0 CBL A:1D8401 1.3 22.0 1.0 FAH A:1D8401 2.1 21.0 1.0 FAF A:1D8401 2.1 24.2 1.0 CBH A:1D8401 2.3 19.8 1.0 CAO A:1D8401 3.1 20.1 1.0 CAR A:1D8401 3.2 18.4 1.0 O A:ASP302 3.3 24.1 1.0 O A:HOH593 3.3 36.3 1.0 CD A:PRO304 3.5 22.3 1.0 CG A:PRO304 4.1 21.4 1.0 C A:ASP302 4.3 30.4 1.0 O A:HOH587 4.3 37.4 1.0 CA A:ILE303 4.3 15.8 1.0 CAK A:1D8401 4.3 19.8 1.0 O A:HOH590 4.4 36.0 1.0 CBD A:1D8401 4.4 18.0 1.0 N A:PRO304 4.6 16.4 1.0 N A:ILE303 4.7 18.7 1.0 CAM A:1D8401 4.9 19.1 1.0 C A:ILE303 4.9 16.6 1.0 OE1 A:GLN241 5.0 21.5 1.0

Fluorine binding site 3 out of 6 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:21.0 occ:1.00 FAH A:1D8401 0.0 21.0 1.0 CBL A:1D8401 1.3 22.0 1.0 FAG A:1D8401 2.1 22.1 1.0 FAF A:1D8401 2.2 24.2 1.0 CBH A:1D8401 2.3 19.8 1.0 CAR A:1D8401 2.7 18.4 1.0 OE1 A:GLN241 3.4 21.5 1.0 CZ A:PHE328 3.5 19.4 1.0 CAO A:1D8401 3.6 20.1 1.0 CE2 A:PHE328 3.6 13.9 1.0 CD A:PRO304 3.7 22.3 1.0 CD A:GLN241 3.9 23.2 1.0 O A:HOH587 3.9 37.4 1.0 CBD A:1D8401 4.1 18.0 1.0 NE2 A:GLN241 4.3 18.5 1.0 CG A:PRO304 4.5 21.4 1.0 CA A:ILE303 4.6 15.8 1.0 CE1 A:PHE328 4.7 19.6 1.0 CAK A:1D8401 4.7 19.8 1.0 O A:ASP302 4.8 24.1 1.0 CG A:GLN241 4.8 15.8 1.0 CD2 A:PHE328 4.8 13.7 1.0 CG1 A:ILE303 4.9 19.0 1.0 CAM A:1D8401 4.9 19.1 1.0 OAB A:1D8401 4.9 16.6 1.0 CG2 A:ILE303 5.0 18.0 1.0 N A:PRO304 5.0 16.4 1.0 CAX A:1D8401 5.0 16.4 1.0

Fluorine binding site 4 out of 6 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:27.9 occ:1.00 FAF B:1D8401 0.0 27.9 1.0 CBL B:1D8401 1.3 26.4 1.0 FAG B:1D8401 2.2 26.5 1.0 FAH B:1D8401 2.2 27.0 1.0 CBH B:1D8401 2.3 24.0 1.0 CAO B:1D8401 2.8 23.8 1.0 CE2 B:PHE328 3.4 16.6 1.0 O B:ASP302 3.4 25.5 1.0 CAR B:1D8401 3.5 23.0 1.0 CZ B:PHE328 3.7 14.3 1.0 CA B:ILE303 3.7 15.5 1.0 CG1 B:ILE303 3.8 16.3 1.0 C B:ASP302 3.9 23.6 1.0 CAK B:1D8401 4.1 23.8 1.0 N B:ILE303 4.1 18.3 1.0 CD B:PRO304 4.2 24.2 1.0 CG2 B:ILE297 4.2 17.6 1.0 CD2 B:PHE328 4.2 14.1 1.0 CB B:ILE303 4.3 17.1 1.0 CBD B:1D8401 4.6 22.6 1.0 CE1 B:PHE328 4.7 11.8 1.0 CG2 B:ILE303 4.8 13.8 1.0 CB B:ASP302 4.8 23.2 1.0 C B:ILE303 4.9 19.1 1.0 CAM B:1D8401 4.9 23.1 1.0 N B:PRO304 4.9 18.8 1.0 CD1 B:ILE297 5.0 17.5 1.0

Fluorine binding site 5 out of 6 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:26.5 occ:1.00 FAG B:1D8401 0.0 26.5 1.0 CBL B:1D8401 1.3 26.4 1.0 FAH B:1D8401 2.1 27.0 1.0 FAF B:1D8401 2.2 27.9 1.0 CBH B:1D8401 2.3 24.0 1.0 CAO B:1D8401 3.0 23.8 1.0 CAR B:1D8401 3.2 23.0 1.0 O B:ASP302 3.3 25.5 1.0 CD B:PRO304 3.6 24.2 1.0 CG B:PRO304 4.0 29.5 1.0 O B:HOH578 4.2 36.1 1.0 CAK B:1D8401 4.3 23.8 1.0 CA B:ILE303 4.4 15.5 1.0 CBD B:1D8401 4.4 22.6 1.0 C B:ASP302 4.4 23.6 1.0 N B:PRO304 4.5 18.8 1.0 CAM B:1D8401 4.8 23.1 1.0 OE1 B:GLN241 4.9 17.9 1.0 N B:ILE303 4.9 18.3 1.0 C B:ILE303 4.9 19.1 1.0

Fluorine binding site 6 out of 6 in the Ebola Virus VP35 Bound to Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Ebola Virus VP35 Bound to Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:27.0 occ:1.00 FAH B:1D8401 0.0 27.0 1.0 CBL B:1D8401 1.3 26.4 1.0 FAG B:1D8401 2.1 26.5 1.0 FAF B:1D8401 2.2 27.9 1.0 CBH B:1D8401 2.3 24.0 1.0 CAR B:1D8401 2.7 23.0 1.0 OE1 B:GLN241 3.2 17.9 1.0 CZ B:PHE328 3.5 14.3 1.0 CAO B:1D8401 3.6 23.8 1.0 CD B:GLN241 3.7 26.4 1.0 CE2 B:PHE328 3.8 16.6 1.0 CD B:PRO304 3.8 24.2 1.0 CBD B:1D8401 4.1 22.6 1.0 NE2 B:GLN241 4.1 20.9 1.0 CG B:GLN241 4.4 13.9 1.0 CG B:PRO304 4.4 29.5 1.0 NE2 B:GLN244 4.7 14.4 0.5 CE1 B:PHE328 4.7 11.8 1.0 CAK B:1D8401 4.7 23.8 1.0 OAB B:1D8401 4.8 22.0 1.0 CA B:ILE303 4.9 15.5 1.0 CAM B:1D8401 4.9 23.1 1.0 CB B:GLN241 4.9 13.7 1.0 O B:ASP302 4.9 25.5 1.0 CAX B:1D8401 4.9 22.6 1.0

C.S.Brown, M.S.Lee, D.W.Leung, T.Wang, W.Xu, P.Luthra, M.Anantpadma, R.S.Shabman, L.M.Melito, K.S.Macmillan, D.M.Borek, Z.Otwinowski, P.Ramanan, A.J.Stubbs, D.S.Peterson, J.M.Binning, M.Tonelli, M.A.Olson, R.A.Davey, J.M.Ready, C.F.Basler, G.K.Amarasinghe. In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity. J.Mol.Biol. V. 426 2045 2014.
ISSN: ISSN 0022-2836
PubMed: 24495995
DOI: 10.1016/J.JMB.2014.01.010