Fluorine in PDB 2qhz: Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease

The structure of Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease, PDB code: 2qhz was solved by C.A.Schiffer, M.N.L.Nalam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.30 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.737, 58.011, 61.840, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.5

The binding sites of Fluorine atom in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease (pdb code 2qhz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease, PDB code: 2qhz:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 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, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:24.1 occ:1.00 F26 A:MZ2200 0.0 24.1 1.0 C25 A:MZ2200 1.3 23.8 1.0 F28 A:MZ2200 2.1 23.7 1.0 F27 A:MZ2200 2.2 25.9 1.0 C23 A:MZ2200 2.4 23.5 1.0 C22 A:MZ2200 2.7 21.6 1.0 O A:ASP30 3.1 20.7 1.0 CB A:ALA28 3.2 19.6 1.0 N A:ASP30 3.5 19.9 1.0 C24 A:MZ2200 3.7 24.2 1.0 CA A:ALA28 3.7 19.5 1.0 CD1 A:ILE84 3.7 20.5 1.0 C A:ASP30 3.8 20.7 1.0 CG2 A:VAL32 3.8 21.3 1.0 N A:ASP29 3.9 19.4 1.0 CB A:ASP30 3.9 20.9 1.0 CA A:ASP30 3.9 20.6 1.0 O A:HOH520 4.0 21.7 1.0 C A:ALA28 4.0 19.5 1.0 C21 A:MZ2200 4.2 21.8 1.0 C A:ASP29 4.6 19.9 1.0 CG A:ASP30 4.7 22.9 1.0 OD2 A:ASP30 4.7 23.3 1.0 CA A:ASP29 4.8 19.9 1.0 N20 A:MZ2200 4.8 18.8 1.0 N A:THR31 4.9 20.6 1.0 CD1 B:ILE50 4.9 21.5 1.0 O A:ALA28 4.9 19.4 1.0 CG1 A:ILE84 4.9 21.0 1.0 O22 A:MZ2200 4.9 19.5 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 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, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:23.7 occ:1.00 F28 A:MZ2200 0.0 23.7 1.0 C25 A:MZ2200 1.3 23.8 1.0 F26 A:MZ2200 2.1 24.1 1.0 F27 A:MZ2200 2.2 25.9 1.0 C23 A:MZ2200 2.3 23.5 1.0 C24 A:MZ2200 2.7 24.2 1.0 CD1 A:ILE47 3.2 23.5 1.0 C22 A:MZ2200 3.4 21.6 1.0 CG2 A:VAL32 3.6 21.3 1.0 OD2 A:ASP30 3.9 23.3 1.0 CB A:ASP30 4.0 20.9 1.0 CB A:ILE47 4.1 23.4 1.0 CG1 A:ILE47 4.2 23.4 1.0 CD1 B:ILE50 4.3 21.5 1.0 CG2 A:ILE47 4.4 24.3 1.0 CG A:ASP30 4.4 22.9 1.0 O A:HOH520 4.6 21.7 1.0 N A:ASP30 4.6 19.9 1.0 O A:ASP30 4.7 20.7 1.0 CA A:ASP30 4.8 20.6 1.0 C21 A:MZ2200 4.8 21.8 1.0 CD1 A:LEU76 4.9 19.3 1.0 C A:ASP30 4.9 20.7 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 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, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:25.9 occ:1.00 F27 A:MZ2200 0.0 25.9 1.0 C25 A:MZ2200 1.3 23.8 1.0 F26 A:MZ2200 2.2 24.1 1.0 F28 A:MZ2200 2.2 23.7 1.0 C23 A:MZ2200 2.4 23.5 1.0 O A:HOH520 2.6 21.7 1.0 C22 A:MZ2200 3.2 21.6 1.0 C24 A:MZ2200 3.3 24.2 1.0 N A:ASP29 3.4 19.4 1.0 N A:ASP30 3.6 19.9 1.0 OD2 A:ASP30 3.8 23.3 1.0 CB A:ASP29 3.9 20.2 1.0 CA A:ASP29 4.1 19.9 1.0 CB A:ASP30 4.1 20.9 1.0 CG A:ASP30 4.1 22.9 1.0 C A:ALA28 4.2 19.5 1.0 CA A:ALA28 4.2 19.5 1.0 C A:ASP29 4.3 19.9 1.0 CA A:ASP30 4.4 20.6 1.0 CB A:ALA28 4.5 19.6 1.0 CG A:ASP29 4.5 21.0 1.0 C21 A:MZ2200 4.5 21.8 1.0 O A:ASP30 4.6 20.7 1.0 OD2 A:ASP29 4.7 22.3 1.0 C A:ASP30 4.9 20.7 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 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 4 of Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:21.9 occ:1.00 F1 A:MZ2200 0.0 21.9 1.0 C7 A:MZ2200 1.3 21.4 1.0 C2 A:MZ2200 2.3 21.9 1.0 C6 A:MZ2200 2.4 21.4 1.0 F2 A:MZ2200 2.7 22.5 1.0 O B:HOH538 3.2 31.4 1.0 O B:GLY48 3.4 21.0 1.0 O B:HOH521 3.4 20.2 1.0 CB B:ILE47 3.5 22.1 1.0 C3 A:MZ2200 3.6 22.0 1.0 N B:GLY48 3.6 21.7 1.0 C5 A:MZ2200 3.7 21.4 1.0 O B:HOH511 3.9 16.6 1.0 CG2 B:ILE47 4.0 23.0 1.0 CA B:ILE47 4.1 22.3 1.0 C4 A:MZ2200 4.1 22.1 1.0 O B:HOH552 4.1 34.3 1.0 C B:ILE47 4.2 22.0 1.0 C B:GLY48 4.2 21.4 1.0 CG1 B:ILE47 4.4 22.1 1.0 CD1 B:ILE47 4.5 22.7 1.0 CA B:GLY48 4.5 21.5 1.0 O A:HOH581 4.9 36.9 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 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 5 of Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:23.1 occ:1.00 F3 A:MZ2200 0.0 23.1 1.0 C4 A:MZ2200 1.3 22.1 1.0 C3 A:MZ2200 2.4 22.0 1.0 C5 A:MZ2200 2.4 21.4 1.0 O10 A:MZ2200 2.8 21.1 1.0 S8 A:MZ2200 3.0 22.2 1.0 CB B:ALA28 3.0 21.4 1.0 C16 A:MZ2200 3.3 20.1 1.0 CG2 B:ILE84 3.5 20.8 1.0 CD1 B:ILE84 3.5 21.5 1.0 N11 A:MZ2200 3.5 21.6 1.0 C6 A:MZ2200 3.6 21.4 1.0 C2 A:MZ2200 3.6 21.9 1.0 CA B:ALA28 3.9 21.4 1.0 CG2 B:VAL32 4.1 21.8 1.0 C7 A:MZ2200 4.1 21.4 1.0 O B:ASP30 4.2 21.4 1.0 OD1 B:ASP25 4.2 23.2 1.0 CB B:ILE84 4.2 21.2 1.0 O9 A:MZ2200 4.3 21.5 1.0 CG1 B:ILE84 4.4 21.2 1.0 C12 A:MZ2200 4.4 21.9 1.0 O B:HOH511 4.6 16.6 1.0 C17 A:MZ2200 4.7 19.6 1.0 F2 A:MZ2200 4.8 22.5 1.0 CD1 A:ILE50 4.8 22.8 1.0 N B:ALA28 4.9 21.1 1.0 C32 A:MZ2200 5.0 20.1 1.0 C B:ALA28 5.0 21.3 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Protease Inhibitor, Mit-1-AC87 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 6 of Crystal Structure of Protease Inhibitor, Mit-1-AC87 in Complex with Wild Type Hiv-1 Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:F200 b:22.5 occ:1.00 F2 A:MZ2200 0.0 22.5 1.0 C2 A:MZ2200 1.4 21.9 1.0 C7 A:MZ2200 2.4 21.4 1.0 C3 A:MZ2200 2.4 22.0 1.0 F1 A:MZ2200 2.7 21.9 1.0 O B:HOH538 3.1 31.4 1.0 OD2 B:ASP30 3.4 29.5 1.0 CB B:ASP30 3.5 22.5 1.0 C6 A:MZ2200 3.6 21.4 1.0 C4 A:MZ2200 3.7 22.1 1.0 O B:HOH511 3.9 16.6 1.0 CG B:ASP30 3.9 25.0 1.0 CD1 B:LEU76 4.0 20.9 1.0 CG2 B:ILE47 4.0 23.0 1.0 N B:ASP30 4.2 21.9 1.0 C5 A:MZ2200 4.2 21.4 1.0 CD1 B:ILE47 4.2 22.7 1.0 CB B:ILE47 4.3 22.1 1.0 CA B:ASP30 4.3 22.2 1.0 O B:ASP30 4.4 21.4 1.0 CG2 B:VAL32 4.4 21.8 1.0 C B:ASP30 4.6 21.6 1.0 F3 A:MZ2200 4.8 23.1 1.0 CG1 B:ILE47 4.9 22.1 1.0

M.D.Altman, A.Ali, G.S.Reddy, M.N.Nalam, S.G.Anjum, H.Cao, S.Chellappan, V.Kairys, M.X.Fernandes, M.K.Gilson, C.A.Schiffer, T.M.Rana, B.Tidor. Hiv-1 Protease Inhibitors From Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants. J.Am.Chem.Soc. V. 130 6099 2008.
ISSN: ISSN 0002-7863
PubMed: 18412349
DOI: 10.1021/JA076558P