Arsenic in PDB 6gmx: Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One

The structure of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One, PDB code: 6gmx was solved by I.Van Molle, X.Lucas, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.00 / 2.53
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.000, 94.000, 365.490, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 36.1

The structure of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One (pdb code 6gmx). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 12 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One, PDB code: 6gmx:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:0.2 occ:0.79 AS A:CAS60 0.0 0.2 0.8 CE2 A:CAS60 2.0 92.7 0.8 CE1 A:CAS60 2.1 89.8 0.8 SG A:CAS60 2.4 49.4 0.8 CB A:CAS60 3.4 31.0 0.8 CA A:CAS60 3.6 30.9 0.8 O A:GLU59 4.0 39.5 1.0 CD2 A:LEU51 4.1 31.0 1.0 N A:CAS60 4.3 31.0 0.8 C A:GLU59 4.4 40.1 1.0 CG A:LYS55 4.4 59.4 1.0 NE2 A:GLN49 4.5 61.8 1.0 CB A:LYS55 4.6 46.3 1.0 C A:CAS60 4.8 30.9 0.8 CD A:LYS55 4.8 56.6 1.0 OE1 A:GLN49 4.9 48.2 1.0 CD A:GLN49 4.9 48.4 1.0

Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:97.5 occ:0.85 AS A:CAS89 0.0 97.5 0.8 CE1 A:CAS89 2.0 85.6 0.8 CE2 A:CAS89 2.0 93.5 0.8 SG A:CAS89 2.2 86.6 0.8 CB A:CAS89 2.8 72.5 0.8 C A:CAS89 3.7 46.2 0.8 CA A:CAS89 3.8 55.4 0.8 N A:ILE90 3.9 42.4 1.0 O A:CAS89 4.0 42.6 0.8 ND1 A:HIS10 4.5 51.3 1.0 C A:ILE90 4.5 45.9 1.0 N A:GLU91 4.6 47.5 1.0 CA A:ILE90 4.7 45.2 1.0 CG A:GLU91 4.7 83.3 1.0 CE1 A:HIS10 4.7 50.6 1.0 O A:ILE90 4.7 42.2 1.0 N A:CAS89 4.8 46.6 0.8 CA A:HIS10 4.9 35.4 1.0

Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:0.4 occ:0.88 AS C:CAS77 0.0 0.4 0.9 CE2 C:CAS77 2.0 0.3 0.9 CE1 C:CAS77 2.0 0.5 0.9 SG C:CAS77 2.2 70.6 0.9 CB C:CAS77 3.1 48.0 0.9 CA C:CAS77 3.6 33.1 0.9 CA C:GLY106 4.1 54.3 1.0 O C:THR105 4.1 68.3 1.0 C C:CAS77 4.2 38.1 0.9 N C:ASN78 4.3 42.4 1.0 N C:GLY106 4.3 61.2 1.0 C C:THR105 4.3 66.2 1.0 CE1 C:PHE148 4.6 87.5 1.0 N C:CAS77 4.8 40.0 0.9 O C:PHE76 4.9 57.9 1.0

Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:0.2 occ:0.78 AS D:CAS60 0.0 0.2 0.8 CE1 D:CAS60 2.0 0.4 0.8 CE2 D:CAS60 2.0 0.8 0.8 SG D:CAS60 2.3 53.6 0.8 CB D:CAS60 3.3 41.9 0.8 CA D:CAS60 3.5 35.0 0.8 CD2 D:LEU51 3.5 62.5 1.0 N D:CAS60 4.2 36.9 0.8 O D:GLU59 4.4 45.5 1.0 NE2 D:GLN49 4.4 61.3 1.0 CB D:LYS55 4.4 65.2 1.0 CG D:LYS55 4.5 58.1 1.0 C D:GLU59 4.5 45.2 1.0 C D:CAS60 4.7 40.2 0.8 CB D:LEU51 4.7 61.2 1.0 CG D:LEU51 4.8 62.5 1.0 CA D:LEU51 4.8 69.8 1.0 O D:CAS60 4.9 47.5 0.8 CD D:GLN49 4.9 53.6 1.0

Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ E:As112 b:0.0 occ:0.70 AS E:CAS112 0.0 0.0 0.7 CE2 E:CAS112 2.0 0.1 0.7 CE1 E:CAS112 2.0 99.8 0.7 SG E:CAS112 2.2 78.0 0.7 CB E:CAS112 2.6 67.4 0.7 CA E:CAS112 3.9 63.4 0.7 CD2 F:LEU158 4.0 39.9 1.0 CE1 E:PHE77 4.1 67.0 1.0 CD1 E:LEU110 4.3 34.2 1.0 OXT E:CAS112 4.4 46.5 0.7 CB E:LEU110 4.4 40.8 1.0 C E:CAS112 4.4 53.4 0.7 CG1 E:VAL73 4.4 45.2 1.0 CZ E:PHE77 4.5 60.4 1.0 CB F:LEU158 4.6 32.3 1.0 CD2 E:TYR76 4.6 37.5 1.0 N E:CAS112 4.9 60.2 0.7 CD1 E:PHE77 4.9 66.0 1.0 CG2 E:VAL73 4.9 31.9 1.0 CB E:SER39 4.9 63.3 1.0 CG F:LEU158 4.9 41.5 1.0

Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:99.4 occ:0.85 AS F:CAS77 0.0 99.4 0.8 CE2 F:CAS77 2.0 90.7 0.8 CE1 F:CAS77 2.0 97.1 0.8 SG F:CAS77 2.2 66.3 0.8 CB F:CAS77 3.2 49.7 0.8 CA F:CAS77 3.8 48.3 0.8 CE H:MET45 4.2 97.0 1.0 CE2 F:PHE148 4.4 86.4 1.0 C F:CAS77 4.4 48.0 0.8 O F:THR105 4.6 55.0 1.0 CA F:GLY106 4.7 52.3 1.0 N F:ASN78 4.7 45.6 1.0 NE F:ARG79 4.8 73.5 1.0 NH2 F:ARG79 4.8 81.7 1.0 N F:GLY106 4.9 62.8 1.0 C F:THR105 4.9 57.0 1.0

Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:0.2 occ:0.76 AS G:CAS60 0.0 0.2 0.8 CE2 G:CAS60 2.0 0.3 0.8 CE1 G:CAS60 2.0 0.6 0.8 SG G:CAS60 2.3 53.3 0.8 CB G:CAS60 3.3 36.7 0.8 CA G:CAS60 3.4 29.9 0.8 CD2 G:LEU51 3.6 56.7 1.0 N G:CAS60 4.1 44.3 0.8 NE2 G:GLN49 4.2 59.5 1.0 CB G:LYS55 4.3 57.5 1.0 CG G:LYS55 4.4 66.4 1.0 O G:GLU59 4.5 56.1 1.0 C G:GLU59 4.6 51.3 1.0 C G:CAS60 4.6 39.2 0.8 O G:CAS60 4.8 41.2 0.8 CD G:GLN49 4.8 60.1 1.0 CG G:LEU51 4.9 55.9 1.0 CB G:LEU51 4.9 61.5 1.0 CD G:LYS55 5.0 68.3 1.0 CA G:LEU51 5.0 62.4 1.0

Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.6 occ:0.83 AS G:CAS89 0.0 0.6 0.8 CE2 G:CAS89 2.0 0.3 0.8 CE1 G:CAS89 2.0 0.6 0.8 SG G:CAS89 2.2 58.4 0.8 CB G:CAS89 3.1 37.3 0.8 CA G:CAS89 3.8 40.7 0.8 N G:ILE90 4.1 39.9 1.0 C G:CAS89 4.1 39.8 0.8 O G:HOH218 4.3 57.2 1.0 O G:ILE90 4.5 40.1 1.0 C G:ILE90 4.7 48.2 1.0

Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 9 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:95.9 occ:0.91 AS I:CAS77 0.0 95.9 0.9 CE2 I:CAS77 2.0 0.1 0.9 CE1 I:CAS77 2.0 97.4 0.9 SG I:CAS77 2.3 67.7 0.9 CB I:CAS77 3.2 43.0 0.9 CA I:CAS77 3.7 33.9 0.9 CA I:GLY106 3.9 44.8 1.0 N I:GLY106 4.1 51.8 1.0 O I:THR105 4.1 45.2 1.0 C I:CAS77 4.3 35.8 0.9 C I:THR105 4.3 52.7 1.0 N I:ASN78 4.5 30.3 1.0 NH2 I:ARG79 4.9 86.5 1.0 N I:CAS77 4.9 37.3 0.9 CE2 I:PHE148 4.9 66.6 1.0 O I:PHE76 5.0 45.1 1.0 O I:GLY104 5.0 52.5 1.0

Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 10 of Pvhl:Elob:Eloc in Complex with 6-Chlorothiochroman-4-One within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:0.1 occ:0.77 AS J:CAS60 0.0 0.1 0.8 CE1 J:CAS60 2.0 0.6 0.8 CE2 J:CAS60 2.0 0.3 0.8 SG J:CAS60 2.3 48.7 0.8 CB J:CAS60 3.3 37.7 0.8 CA J:CAS60 3.5 30.5 0.8 CD2 J:LEU51 3.8 43.8 1.0 N J:CAS60 4.2 30.5 0.8 O J:GLU59 4.3 47.5 1.0 CG J:LYS55 4.4 43.7 1.0 CB J:LYS55 4.4 43.6 1.0 C J:GLU59 4.5 49.0 1.0 NE2 J:GLN49 4.6 60.9 1.0 C J:CAS60 4.6 39.6 0.8 CB J:LEU51 4.7 36.0 1.0 O J:CAS60 4.8 43.4 0.8 CA J:LEU51 4.8 38.2 1.0 CG J:LEU51 4.9 39.0 1.0 CD J:LYS55 5.0 35.3 1.0

X.Lucas, I.Van Molle, A.Ciulli. Surface Probing By Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase. J. Med. Chem. V. 61 7387 2018.
ISSN: ISSN 1520-4804
PubMed: 30040896
DOI: 10.1021/ACS.JMEDCHEM.8B00842