Arsenic in PDB 6lmi: Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid

The structure of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid, PDB code: 6lmi was solved by S.Sugiyama, T.Iwaki, Y.Tamura, K.Tomita, E.Matsuoka, S.Arita, T.Seki, T.Yoshinaga, T.Kawasuji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.926, 71.926, 65.798, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.4

The binding sites of Arsenic atom in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid (pdb code 6lmi). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid, PDB code: 6lmi:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As65 b:40.0 occ:1.00 AS A:CAF65 0.0 40.0 1.0 O1 A:CAF65 1.7 41.3 1.0 CE1 A:CAF65 2.0 39.4 1.0 SG A:CAF65 2.2 38.6 1.0 CB A:CAF65 3.0 38.4 1.0 N A:CAF65 3.4 38.4 1.0 OD1 A:ASN120 3.5 36.4 1.0 ND2 A:ASN120 3.7 31.0 1.0 CG A:ASN120 3.7 36.6 1.0 CA A:CAF65 3.8 38.9 1.0 OE1 A:GLU92 3.8 55.6 1.0 O A:HOH420 3.8 41.8 1.0 C A:ASP64 4.1 37.8 1.0 CG A:GLU92 4.2 48.1 1.0 CD A:GLU92 4.3 50.6 1.0 OG1 A:THR97 4.6 34.2 1.0 O A:ASP64 4.7 38.9 1.0 CA A:ASP64 4.7 38.7 1.0 CB A:ASN120 4.8 37.4 1.0 O A:HOH403 4.9 34.1 1.0 CG A:LEU74 4.9 38.8 1.0

Arsenic binding site 2 out of 2 in the Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1-Benzopyran-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As130 b:51.4 occ:1.00 AS A:CAF130 0.0 51.4 1.0 O1 A:CAF130 1.7 50.7 1.0 CE1 A:CAF130 2.0 51.6 1.0 SG A:CAF130 2.2 42.4 1.0 CB A:CAF130 3.0 37.3 1.0 O A:ILE135 4.2 38.0 1.0 CA A:CAF130 4.4 33.2 1.0 CG2 A:ILE135 4.5 34.2 1.0 O A:LYS136 4.6 46.5 1.0 C A:LYS136 4.7 46.5 1.0 N A:GLN137 4.7 51.4 1.0 CG1 A:VAL126 4.7 35.6 1.0 CB A:ILE135 4.8 35.0 1.0 CD2 A:PHE121 4.8 48.4 1.0 C A:ILE135 4.8 36.2 1.0 CG A:PHE121 4.8 47.6 1.0 CA A:GLN137 4.9 60.9 1.0 CB A:GLN137 4.9 61.2 1.0 CB A:PHE121 5.0 43.1 1.0

S.Sugiyama, T.Iwaki, Y.Tamura, K.Tomita, E.Matsuoka, S.Arita, T.Seki, T.Yoshinaga, T.Kawasuji. Discovery of Novel Integrase-Ledgf/P75 Allosteric Inhibitors Based on A Benzene Scaffold. Bioorg.Med.Chem. V. 28 15643 2020.
ISSN: ESSN 1464-3391
PubMed: 32773094
DOI: 10.1016/J.BMC.2020.115643