Fluorine in PDB 7lpw: Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189

All present enzymatic activity of Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189:
2.7.7.49;

The structure of Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189, PDB code: 7lpw was solved by N.Losada, F.X.Ruiz, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.82 / 2.32
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.433, 72.953, 107.747, 90, 99.87, 90
R / Rfree (%)	21.5 / 24.8

The binding sites of Fluorine atom in the Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189 (pdb code 7lpw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189, PDB code: 7lpw:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189


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 Hiv-1 Rt in Complex with Nbd-14189 within 5.0Å range: probe atom residue distance (Å) B Occ A:F605 b:118.7 occ:1.00 F01 A:YBA605 0.0 118.7 1.0 C02 A:YBA605 1.4 108.8 1.0 F03 A:YBA605 2.2 110.5 1.0 F04 A:YBA605 2.2 105.6 1.0 C05 A:YBA605 2.4 108.1 1.0 C29 A:YBA605 2.7 106.4 1.0 CD2 A:LEU100 3.1 82.9 1.0 C06 A:YBA605 3.7 107.7 1.0 CB A:PRO95 3.9 65.2 1.0 C28 A:YBA605 4.1 106.3 1.0 F07 A:YBA605 4.2 109.7 1.0 CH2 A:TRP229 4.2 82.6 1.0 CG A:LEU100 4.3 84.4 1.0 CG A:PRO95 4.3 65.1 1.0 CD1 A:LEU100 4.4 83.9 1.0 CZ3 A:TRP229 4.5 84.9 1.0 CD2 A:TYR181 4.6 78.2 1.0 CD1 A:TYR188 4.7 80.9 1.0 CG A:TYR188 4.7 79.8 1.0 C08 A:YBA605 4.8 106.2 1.0 CZ2 A:TRP229 4.8 81.9 1.0 CB A:TYR181 4.9 80.8 1.0 C09 A:YBA605 4.9 105.3 1.0 CE1 A:TYR188 5.0 81.5 1.0 CB A:TYR188 5.0 84.0 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189


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 Hiv-1 Rt in Complex with Nbd-14189 within 5.0Å range: probe atom residue distance (Å) B Occ A:F605 b:110.5 occ:1.00 F03 A:YBA605 0.0 110.5 1.0 C02 A:YBA605 1.4 108.8 1.0 F01 A:YBA605 2.2 118.7 1.0 F04 A:YBA605 2.2 105.6 1.0 C05 A:YBA605 2.4 108.1 1.0 CG A:PRO95 2.9 65.1 1.0 F07 A:YBA605 2.9 109.7 1.0 C06 A:YBA605 3.0 107.7 1.0 CB A:PRO95 3.3 65.2 1.0 C29 A:YBA605 3.4 106.4 1.0 CB A:TYR183 3.6 106.1 1.0 CH2 A:TRP229 3.6 82.6 1.0 CD A:PRO95 3.8 74.7 1.0 CZ2 A:TRP229 3.8 81.9 1.0 CG A:TYR183 4.0 106.6 1.0 CD2 A:TYR183 4.1 106.1 1.0 C08 A:YBA605 4.3 106.2 1.0 C28 A:YBA605 4.6 106.3 1.0 CZ3 A:TRP229 4.6 84.9 1.0 CA A:PRO95 4.7 70.5 1.0 N A:PRO95 4.8 77.4 1.0 CE2 A:TRP229 4.9 85.4 1.0 C09 A:YBA605 4.9 105.3 1.0 CB A:TYR181 4.9 80.8 1.0 CA A:TYR183 5.0 105.5 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189


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 Hiv-1 Rt in Complex with Nbd-14189 within 5.0Å range: probe atom residue distance (Å) B Occ A:F605 b:105.6 occ:1.00 F04 A:YBA605 0.0 105.6 1.0 C02 A:YBA605 1.4 108.8 1.0 F03 A:YBA605 2.2 110.5 1.0 F01 A:YBA605 2.2 118.7 1.0 C05 A:YBA605 2.4 108.1 1.0 F07 A:YBA605 2.8 109.7 1.0 C06 A:YBA605 2.9 107.7 1.0 CB A:TYR181 3.1 80.8 1.0 C29 A:YBA605 3.5 106.4 1.0 CB A:TYR188 3.5 84.0 1.0 CG A:TYR188 3.8 79.8 1.0 CD2 A:TYR181 3.9 78.2 1.0 CG A:TYR181 4.0 78.3 1.0 C08 A:YBA605 4.2 106.2 1.0 CD2 A:TYR188 4.3 77.2 1.0 CD1 A:TYR188 4.3 80.9 1.0 CA A:TYR181 4.4 82.8 1.0 C A:TYR181 4.4 85.1 1.0 CB A:TYR183 4.6 106.1 1.0 C28 A:YBA605 4.6 106.3 1.0 N A:GLN182 4.7 91.9 1.0 O A:TYR181 4.7 81.9 1.0 CG A:PRO95 4.8 65.1 1.0 CD2 A:LEU100 4.8 82.9 1.0 CA A:TYR188 4.9 83.8 1.0 C09 A:YBA605 4.9 105.3 1.0 CB A:PRO95 5.0 65.2 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Hiv-1 Rt in Complex with Nbd-14189


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 Hiv-1 Rt in Complex with Nbd-14189 within 5.0Å range: probe atom residue distance (Å) B Occ A:F605 b:109.7 occ:1.00 F07 A:YBA605 0.0 109.7 1.0 C06 A:YBA605 1.4 107.7 1.0 C08 A:YBA605 2.4 106.2 1.0 C05 A:YBA605 2.4 108.1 1.0 F04 A:YBA605 2.8 105.6 1.0 C02 A:YBA605 2.8 108.8 1.0 F03 A:YBA605 2.9 110.5 1.0 CB A:TYR183 3.1 106.1 1.0 N A:TYR183 3.6 105.7 1.0 C09 A:YBA605 3.6 105.3 1.0 C29 A:YBA605 3.6 106.4 1.0 O A:TYR183 3.8 104.0 1.0 CA A:TYR183 3.8 105.5 1.0 CD2 A:TYR183 4.0 106.1 1.0 CG A:TYR183 4.1 106.6 1.0 C28 A:YBA605 4.1 106.3 1.0 F01 A:YBA605 4.2 118.7 1.0 C A:TYR183 4.2 105.2 1.0 CB A:TYR188 4.3 84.0 1.0 CB A:ASP186 4.5 99.1 1.0 O A:ASP186 4.5 89.8 1.0 CZ2 A:TRP229 4.5 81.9 1.0 C A:GLN182 4.6 102.4 1.0 N A:TYR188 4.8 86.5 1.0 C A:ASP186 4.8 94.9 1.0 CA A:GLN182 4.9 99.5 1.0 C10 A:YBA605 4.9 103.8 1.0 O A:TYR181 4.9 81.9 1.0 N A:GLN182 4.9 91.9 1.0 CE2 A:TRP229 5.0 85.4 1.0 C A:TYR181 5.0 85.1 1.0

N.Losada, F.X.Ruiz, F.Curreli, K.Gruber, A.Pilch, K.Das, A.K.Debnath, E.Arnold. Hiv-1 GP120 Antagonists Also Inhibit Hiv-1 Reverse Transcriptase By Bridging the Nnrti and Nrti Sites. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34735153
DOI: 10.1021/ACS.JMEDCHEM.1C01104