Fluorine in PDB 3gi6: Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease

The structure of Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease, PDB code: 3gi6 was solved by M.N.L.Nalam, C.A.Schiffer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.00 / 1.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.803, 58.021, 61.671, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.6

The binding sites of Fluorine atom in the Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease (pdb code 3gi6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease, PDB code: 3gi6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease


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 Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:24.8 occ:1.00 F1 A:D78200 0.0 24.8 1.0 C46 A:D78200 1.3 22.5 1.0 F2 A:D78200 2.1 24.3 1.0 F3 A:D78200 2.1 25.0 1.0 C41 A:D78200 2.3 22.4 1.0 C42 A:D78200 3.1 21.6 1.0 C40 A:D78200 3.3 22.4 1.0 CG B:PRO81 3.6 22.3 1.0 CB B:PRO81 3.8 22.3 1.0 C35 A:D78200 4.0 20.6 1.0 O B:HOH143 4.2 43.1 1.0 O A:HOH162 4.3 53.8 1.0 C43 A:D78200 4.4 21.5 1.0 C45 A:D78200 4.5 22.2 1.0 C34 A:D78200 4.8 21.5 1.0 C36 A:D78200 4.9 21.7 1.0 C44 A:D78200 4.9 22.8 1.0 CD B:PRO81 5.0 21.6 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease


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 Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:24.3 occ:1.00 F2 A:D78200 0.0 24.3 1.0 C46 A:D78200 1.3 22.5 1.0 F1 A:D78200 2.1 24.8 1.0 F3 A:D78200 2.1 25.0 1.0 C41 A:D78200 2.3 22.4 1.0 C40 A:D78200 2.7 22.4 1.0 CZ A:PHE53 3.5 22.3 1.0 C42 A:D78200 3.6 21.6 1.0 CE1 A:PHE53 4.0 23.3 1.0 C45 A:D78200 4.1 22.2 1.0 CE2 A:PHE53 4.5 23.1 1.0 CA A:GLY48 4.6 22.8 1.0 O A:HOH162 4.7 53.8 1.0 C43 A:D78200 4.8 21.5 1.0 O A:HOH151 4.9 26.0 1.0 C44 A:D78200 4.9 22.8 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease


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 Protease Inhibitor, AD78 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:25.0 occ:1.00 F3 A:D78200 0.0 25.0 1.0 C46 A:D78200 1.3 22.5 1.0 F2 A:D78200 2.1 24.3 1.0 F1 A:D78200 2.1 24.8 1.0 C41 A:D78200 2.3 22.4 1.0 C42 A:D78200 2.8 21.6 1.0 C A:GLY48 3.3 22.8 1.0 CA A:GLY48 3.4 22.8 1.0 N A:GLY49 3.4 22.2 1.0 C40 A:D78200 3.5 22.4 1.0 O A:HOH162 3.6 53.8 1.0 O A:GLY49 3.7 20.9 1.0 O A:GLY48 3.9 23.7 1.0 CE1 A:PHE53 4.0 23.3 1.0 CZ A:PHE53 4.0 22.3 1.0 CA A:GLY49 4.1 21.9 1.0 C43 A:D78200 4.2 21.5 1.0 C A:GLY49 4.2 21.6 1.0 N A:GLY48 4.4 22.5 1.0 C35 A:D78200 4.7 20.6 1.0 C45 A:D78200 4.7 22.2 1.0 CG B:PRO81 4.7 22.3 1.0 CE2 A:PHE53 4.8 23.1 1.0 CD1 A:PHE53 4.8 23.2 1.0 C44 A:D78200 4.9 22.8 1.0

M.N.Nalam, A.Ali, M.D.Altman, G.S.Reddy, S.Chellappan, V.Kairys, A.Ozen, H.Cao, M.K.Gilson, B.Tidor, T.M.Rana, C.A.Schiffer. Evaluating the Substrate-Envelope Hypothesis: Structural Analysis of Novel Hiv-1 Protease Inhibitors Designed to Be Robust Against Drug Resistance. J.Virol. V. 84 5368 2010.
ISSN: ISSN 0022-538X
PubMed: 20237088
DOI: 10.1128/JVI.02531-09