Arsenic in PDB 6lmq: Crystal Structure of Hiv-1 Integrase Catalytic Core Domain in Complex with 2-(Tert-Butoxy)-2-[3-(3,4-Dihydro-2H-1,4-Benzoxazin-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-1,4-Benzoxazin-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid, PDB code: 6lmq 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)	62.25 / 2.10
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.885, 71.885, 65.520, 90.00, 90.00, 120.00
R / Rfree (%)	21.2 / 24

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-1,4-Benzoxazin-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid (pdb code 6lmq). 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-1,4-Benzoxazin-6-Yl)-6- Methanesulfonamido-2,3',4',5-Tetramethyl-[1,1'-Biphenyl]-4-Yl]Acetic Acid, PDB code: 6lmq:
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-1,4-Benzoxazin-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-1,4-Benzoxazin-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:28.6 occ:0.60 AS A:CAF65 0.0 28.6 0.6 O1 A:CAF65 1.7 33.8 0.6 CE1 A:CAF65 1.9 27.6 0.6 SG A:CAF65 2.2 23.6 0.6 CB A:CAF65 3.0 22.6 0.6 ND2 A:ASN120 3.4 32.7 1.0 N A:CAF65 3.4 23.5 0.6 OD1 A:ASN120 3.5 38.3 1.0 CG A:ASN120 3.6 37.8 1.0 CA A:CAF65 3.7 24.7 0.6 O A:HOH417 3.8 32.5 1.0 OE1 A:GLU92 3.8 51.7 1.0 CG A:GLU92 3.9 44.7 1.0 C A:ASP64 4.1 27.5 1.0 CD A:GLU92 4.2 48.6 1.0 OG1 A:THR97 4.6 34.5 1.0 CB A:ASN120 4.7 33.6 1.0 O A:ASP64 4.7 30.2 1.0 CA A:ASP64 4.8 28.3 1.0 CG A:LEU74 5.0 31.4 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-1,4-Benzoxazin-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-1,4-Benzoxazin-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:47.1 occ:1.00 AS A:CAF130 0.0 47.1 1.0 O1 A:CAF130 1.7 46.6 1.0 CE1 A:CAF130 2.0 49.2 1.0 SG A:CAF130 2.3 30.3 1.0 CB A:CAF130 3.0 26.3 1.0 N A:GLN137 4.2 51.5 1.0 O A:ILE135 4.2 33.7 1.0 CG2 A:ILE135 4.2 30.6 1.0 C A:LYS136 4.4 46.8 1.0 CA A:CAF130 4.4 25.1 1.0 CB A:GLN137 4.5 56.0 1.0 CA A:GLN137 4.5 57.7 1.0 C A:ILE135 4.6 34.2 1.0 CB A:ILE135 4.6 30.5 1.0 O A:LYS136 4.7 44.1 1.0 CA A:LYS136 4.8 44.5 1.0 CG1 A:VAL126 4.9 27.4 1.0 CD2 A:PHE121 4.9 35.2 1.0 N A:LYS136 5.0 39.2 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