Arsenic in PDB 6gmq: Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol

The structure of Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol, PDB code: 6gmq 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)	29.67 / 2.76
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.830, 93.830, 363.820, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 27.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol (pdb code 6gmq). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 14 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol, PDB code: 6gmq:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:0.1 occ:1.00 AS A:CAS60 0.0 0.1 1.0 CE2 A:CAS60 2.0 0.7 1.0 CE1 A:CAS60 2.0 0.2 1.0 SG A:CAS60 2.3 45.8 1.0 CB A:CAS60 3.3 39.6 1.0 CA A:CAS60 3.5 31.4 1.0 CD2 A:LEU51 4.0 38.6 1.0 N A:CAS60 4.0 31.3 1.0 CB A:LYS55 4.2 38.9 1.0 CG A:LYS55 4.4 40.7 1.0 C A:GLU59 4.4 39.8 1.0 O A:GLU59 4.4 33.3 1.0 CD A:LYS55 4.7 49.5 1.0 C A:CAS60 4.8 32.6 1.0 NE2 A:GLN49 5.0 37.4 1.0

Arsenic binding site 2 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:98.9 occ:1.00 AS A:CAS89 0.0 98.9 1.0 CE1 A:CAS89 2.0 0.3 1.0 CE2 A:CAS89 2.0 89.8 1.0 SG A:CAS89 2.2 77.2 1.0 CB A:CAS89 3.0 57.9 1.0 CA A:CAS89 3.9 47.6 1.0 C A:CAS89 4.2 40.8 1.0 N A:ILE90 4.3 37.9 1.0 C A:ILE90 4.8 33.1 1.0 O A:CAS89 4.8 45.5 1.0 N A:GLU91 4.8 37.1 1.0 O A:ILE90 5.0 35.2 1.0

Arsenic binding site 3 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ B:As112 b:82.8 occ:1.00 AS B:CAS112 0.0 82.8 1.0 CE2 B:CAS112 2.0 81.8 1.0 CE1 B:CAS112 2.0 100.0 1.0 SG B:CAS112 2.2 65.7 1.0 CB B:CAS112 2.9 54.3 1.0 CE1 B:PHE77 4.0 34.2 1.0 CG1 B:VAL73 4.0 34.3 1.0 CD1 B:LEU110 4.1 35.0 1.0 CB B:LEU110 4.3 35.7 1.0 CA B:CAS112 4.3 54.7 1.0 CZ B:PHE77 4.3 34.2 1.0 CD2 C:LEU158 4.5 36.1 1.0 C B:CAS112 4.8 55.9 1.0 CB B:SER39 4.8 69.3 1.0 N B:CAS112 4.8 41.9 1.0 CG B:LEU110 4.8 37.1 1.0 CD1 B:PHE77 4.9 34.0 1.0 CB C:LEU158 5.0 40.6 1.0 OXT B:CAS112 5.0 48.0 1.0

Arsenic binding site 4 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:96.7 occ:1.00 AS C:CAS77 0.0 96.7 1.0 CE2 C:CAS77 2.0 97.3 1.0 CE1 C:CAS77 2.0 0.1 1.0 SG C:CAS77 2.2 81.0 1.0 CB C:CAS77 3.2 71.8 1.0 CA C:CAS77 3.5 58.6 1.0 O C:THR105 4.1 65.8 1.0 C C:CAS77 4.2 54.6 1.0 N C:ASN78 4.2 37.8 1.0 CZ C:PHE148 4.4 88.3 1.0 SD K:MET45 4.5 65.2 1.0 NH1 C:ARG79 4.6 76.5 1.0 N C:CAS77 4.7 44.8 1.0 O C:GLY104 4.8 57.8 1.0 C C:THR105 4.9 68.8 1.0 CA C:GLY106 4.9 79.2 1.0

Arsenic binding site 5 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:0.4 occ:1.00 AS D:CAS60 0.0 0.4 1.0 CE1 D:CAS60 2.0 0.7 1.0 CE2 D:CAS60 2.0 0.9 1.0 SG D:CAS60 2.3 53.8 1.0 CB D:CAS60 3.2 32.9 1.0 CA D:CAS60 3.5 32.8 1.0 CD2 D:LEU51 3.7 65.5 1.0 N D:CAS60 4.1 38.0 1.0 NE2 D:GLN49 4.4 59.4 1.0 CB D:LYS55 4.4 58.5 1.0 CG D:LYS55 4.4 56.4 1.0 O D:GLU59 4.6 47.7 1.0 C D:GLU59 4.6 42.4 1.0 C D:CAS60 4.7 35.7 1.0 CD D:GLN49 4.9 53.8 1.0 O D:CAS60 4.9 36.9 1.0 CD D:LYS55 5.0 61.0 1.0

Arsenic binding site 6 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.6 occ:1.00 AS D:CAS89 0.0 0.6 1.0 CE2 D:CAS89 2.0 0.1 1.0 CE1 D:CAS89 2.0 1.0 1.0 SG D:CAS89 2.2 88.5 1.0 CB D:CAS89 3.1 87.3 1.0 CA D:CAS89 4.0 84.7 1.0 N D:ILE90 4.3 77.0 1.0 C D:CAS89 4.4 76.8 1.0 C D:ILE90 4.7 58.9 1.0 O D:ILE90 4.7 54.2 1.0 CG D:GLU91 4.8 88.2 1.0 N D:GLU91 4.8 64.8 1.0

Arsenic binding site 7 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ E:As112 b:87.2 occ:1.00 AS E:CAS112 0.0 87.2 1.0 CE2 E:CAS112 2.0 93.7 1.0 CE1 E:CAS112 2.0 96.7 1.0 SG E:CAS112 2.2 77.1 1.0 CB E:CAS112 2.8 56.1 1.0 CE1 E:PHE77 4.0 46.3 1.0 CD1 E:LEU110 4.1 38.5 1.0 CB E:LEU110 4.1 38.9 1.0 CA E:CAS112 4.2 62.0 1.0 OXT E:CAS112 4.4 52.7 1.0 C E:CAS112 4.5 59.9 1.0 CD2 F:LEU158 4.5 40.3 1.0 CZ E:PHE77 4.6 39.5 1.0 N E:CAS112 4.7 47.5 1.0 CB E:SER39 4.7 64.7 1.0 CG E:LEU110 4.8 38.8 1.0 CG1 E:VAL73 4.8 37.5 1.0 CB F:LEU158 4.8 38.0 1.0 CD1 E:PHE77 4.8 49.5 1.0 O E:LEU110 4.9 51.4 1.0 CD2 E:TYR76 4.9 37.9 1.0 CA E:ALA107 4.9 49.1 1.0

Arsenic binding site 8 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:0.9 occ:1.00 AS F:CAS77 0.0 0.9 1.0 CE2 F:CAS77 2.0 0.4 1.0 CE1 F:CAS77 2.0 0.1 1.0 SG F:CAS77 2.2 99.6 1.0 CB F:CAS77 3.3 92.4 1.0 CA F:CAS77 3.6 77.1 1.0 N F:ASN78 4.1 56.9 1.0 C F:CAS77 4.1 63.8 1.0 O F:THR105 4.2 69.6 1.0 CE H:MET45 4.3 83.9 1.0 O F:GLY104 4.6 63.0 1.0 CZ F:PHE148 4.8 0.6 1.0 N F:CAS77 4.9 66.7 1.0 C F:THR105 4.9 80.7 1.0 CA F:GLY106 4.9 87.4 1.0 NE F:ARG79 4.9 81.5 1.0 O F:PHE76 5.0 64.2 1.0

Arsenic binding site 9 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:77.3 occ:1.00 AS G:CAS60 0.0 77.3 1.0 CE2 G:CAS60 2.0 79.6 1.0 CE1 G:CAS60 2.0 90.8 1.0 SG G:CAS60 2.2 58.9 1.0 CB G:CAS60 3.3 46.7 1.0 CA G:CAS60 3.6 45.1 1.0 CD2 G:LEU51 3.7 54.0 1.0 NE2 G:GLN49 4.1 56.0 1.0 N G:CAS60 4.2 42.1 1.0 CB G:LYS55 4.6 54.9 1.0 CG G:LYS55 4.7 52.2 1.0 CD G:GLN49 4.7 62.8 1.0 C G:GLU59 4.8 47.8 1.0 O G:GLU59 4.8 54.2 1.0

Arsenic binding site 10 out of 14 in the Pvhl:Elob:Eloc in Complex with (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol


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 (4-(1H-Pyrrol-1-Yl)Phenyl)Methanol within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:90.3 occ:1.00 AS G:CAS89 0.0 90.3 1.0 CE2 G:CAS89 2.0 97.7 1.0 CE1 G:CAS89 2.0 92.9 1.0 SG G:CAS89 2.2 64.4 1.0 CB G:CAS89 2.9 50.5 1.0 CA G:CAS89 3.7 42.6 1.0 N G:ILE90 4.1 31.0 1.0 C G:CAS89 4.1 42.0 1.0 O G:ILE90 4.7 42.5 1.0 C G:ILE90 4.7 42.6 1.0 OE2 G:GLU91 4.8 56.6 1.0 O G:CAS89 5.0 39.0 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