Arsenic in PDB 5nvy: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11), PDB code: 5nvy was solved by P.Soares, M.S.Gadd, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 2.90
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.085, 93.085, 362.983, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 26.9

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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) (pdb code 5nvy). 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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11), PDB code: 5nvy:
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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:92.1 occ:1.00 AS A:CAS60 0.0 92.1 1.0 CE1 A:CAS60 2.0 84.8 1.0 CE2 A:CAS60 2.0 82.1 1.0 SG A:CAS60 2.3 66.8 1.0 CB A:CAS60 3.3 55.7 1.0 CA A:CAS60 3.4 52.9 1.0 CD2 A:LEU51 4.0 48.9 1.0 N A:CAS60 4.0 51.6 1.0 O A:GLU59 4.2 53.2 1.0 C A:GLU59 4.4 52.4 1.0 CB A:LYS55 4.7 49.0 1.0 NE2 A:GLN49 4.7 57.3 1.0 C A:CAS60 4.7 50.5 1.0 CG A:LYS55 4.8 52.0 1.0 CB A:LEU51 4.9 48.0 1.0 CA A:LEU51 5.0 49.9 1.0 CG A:LEU51 5.0 47.4 1.0

Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:0.8 occ:1.00 AS A:CAS89 0.0 0.8 1.0 CE1 A:CAS89 2.0 0.3 1.0 CE2 A:CAS89 2.0 0.2 1.0 SG A:CAS89 2.2 91.5 1.0 CB A:CAS89 3.1 78.0 1.0 CA A:CAS89 3.6 68.8 1.0 O A:HOH244 4.0 56.0 1.0 OE2 A:GLU91 4.1 67.0 1.0 C A:CAS89 4.3 62.4 1.0 N A:ILE90 4.3 59.1 1.0 N A:CAS89 4.9 65.8 1.0 O A:ILE90 4.9 56.0 1.0 O A:LEU88 5.0 66.0 1.0

Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:71.2 occ:1.00 AS C:CAS77 0.0 71.2 1.0 CE2 C:CAS77 2.0 74.5 1.0 CE1 C:CAS77 2.0 69.7 1.0 SG C:CAS77 2.2 62.2 1.0 CB C:CAS77 3.1 56.6 1.0 CA C:CAS77 3.6 52.5 1.0 O C:THR105 4.3 53.5 1.0 C C:CAS77 4.3 50.5 1.0 CA C:GLY106 4.4 55.6 1.0 CZ K:PHE109 4.5 70.6 1.0 N C:ASN78 4.5 49.5 1.0 C C:THR105 4.5 55.3 1.0 CZ C:PHE148 4.5 77.6 1.0 CE K:MET45 4.6 88.9 1.0 N C:GLY106 4.6 56.5 1.0 N C:CAS77 4.9 49.7 1.0 SD K:MET45 4.9 90.9 1.0

Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:82.7 occ:1.00 AS D:CAS60 0.0 82.7 1.0 CE1 D:CAS60 2.0 80.8 1.0 CE2 D:CAS60 2.0 81.1 1.0 SG D:CAS60 2.3 67.6 1.0 CB D:CAS60 3.2 60.3 1.0 CA D:CAS60 3.5 57.5 1.0 N D:CAS60 4.1 57.1 1.0 CD2 D:LEU51 4.1 58.4 1.0 O D:HOH211 4.2 56.7 1.0 O D:GLU59 4.5 59.1 1.0 NE2 D:GLN49 4.6 60.2 1.0 C D:GLU59 4.6 58.1 1.0 CB D:LYS55 4.6 65.7 1.0 CG D:LYS55 4.6 68.7 1.0 C D:CAS60 4.8 54.4 1.0 CD D:GLN49 4.9 59.0 1.0

Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.8 occ:1.00 AS D:CAS89 0.0 0.8 1.0 CE1 D:CAS89 2.0 0.4 1.0 CE2 D:CAS89 2.0 0.2 1.0 SG D:CAS89 2.2 1.0 1.0 CB D:CAS89 3.1 0.3 1.0 CA D:CAS89 3.7 99.6 1.0 C D:CAS89 4.2 93.6 1.0 N D:ILE90 4.2 87.4 1.0 OE2 D:GLU91 4.3 0.3 1.0 O D:ILE90 4.7 78.2 1.0 C D:ILE90 4.8 79.0 1.0 O D:CAS89 5.0 95.6 1.0 N D:CAS89 5.0 93.7 1.0

Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:81.9 occ:1.00 AS F:CAS77 0.0 81.9 1.0 CE2 F:CAS77 2.0 85.0 1.0 CE1 F:CAS77 2.0 80.9 1.0 SG F:CAS77 2.2 75.9 1.0 CB F:CAS77 3.3 66.0 1.0 CA F:CAS77 3.8 60.7 1.0 CA F:GLY106 4.3 58.1 1.0 CE H:MET45 4.3 98.2 1.0 N F:GLY106 4.4 59.0 1.0 O F:THR105 4.4 55.7 1.0 C F:CAS77 4.4 57.2 1.0 C F:THR105 4.4 58.1 1.0 CZ F:PHE148 4.6 68.9 1.0 N F:ASN78 4.7 55.4 1.0 NH2 F:ARG79 4.8 72.5 1.0 SD H:MET45 4.9 99.0 1.0 CZ H:PHE109 4.9 96.2 1.0 CE2 F:PHE148 4.9 67.4 1.0 CZ F:ARG79 4.9 70.5 1.0

Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:86.8 occ:1.00 AS G:CAS60 0.0 86.8 1.0 CE2 G:CAS60 2.0 84.0 1.0 CE1 G:CAS60 2.0 86.0 1.0 SG G:CAS60 2.3 73.5 1.0 CB G:CAS60 3.2 66.5 1.0 CA G:CAS60 3.5 64.9 1.0 NE2 G:GLN49 4.0 65.0 1.0 N G:CAS60 4.1 64.8 1.0 CD2 G:LEU51 4.3 66.4 1.0 CG G:LYS55 4.5 74.2 1.0 CB G:LYS55 4.5 71.7 1.0 C G:GLU59 4.6 65.8 1.0 O G:GLU59 4.6 66.3 1.0 CD G:GLN49 4.6 64.5 1.0 C G:CAS60 4.9 63.2 1.0 OE1 G:GLN49 5.0 63.9 1.0

Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.9 occ:1.00 AS G:CAS89 0.0 0.9 1.0 CE2 G:CAS89 2.0 0.7 1.0 CE1 G:CAS89 2.0 0.5 1.0 SG G:CAS89 2.2 92.6 1.0 CB G:CAS89 3.2 82.1 1.0 CA G:CAS89 3.8 73.7 1.0 N G:ILE90 4.1 63.6 1.0 C G:CAS89 4.3 67.5 1.0 C G:ILE90 4.7 59.7 1.0 O G:ILE90 4.7 60.7 1.0 N G:GLU91 4.8 58.6 1.0

Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:65.7 occ:1.00 AS I:CAS77 0.0 65.7 1.0 CE2 I:CAS77 2.0 67.0 1.0 CE1 I:CAS77 2.0 67.5 1.0 SG I:CAS77 2.2 59.0 1.0 CB I:CAS77 3.2 51.5 1.0 CA I:CAS77 3.6 47.7 1.0 O I:THR105 3.7 44.4 1.0 CA I:GLY106 4.0 45.6 1.0 C I:THR105 4.0 45.5 1.0 N I:GLY106 4.1 46.3 1.0 C I:CAS77 4.2 46.5 1.0 N I:ASN78 4.2 46.6 1.0 N I:CAS77 4.9 45.7 1.0 CA I:THR105 5.0 46.8 1.0

Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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 (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:93.2 occ:1.00 AS J:CAS60 0.0 93.2 1.0 CE1 J:CAS60 2.0 89.9 1.0 CE2 J:CAS60 2.0 86.3 1.0 SG J:CAS60 2.3 74.7 1.0 CB J:CAS60 3.3 59.6 1.0 CA J:CAS60 3.5 56.1 1.0 CD2 J:LEU51 4.1 49.7 1.0 N J:CAS60 4.1 54.2 1.0 NE2 J:GLN49 4.4 54.7 1.0 O J:GLU59 4.4 55.1 1.0 C J:GLU59 4.5 54.7 1.0 CB J:LYS55 4.7 56.0 1.0 C J:CAS60 4.8 53.1 1.0 CG J:LYS55 4.8 59.0 1.0 CD J:GLN49 4.9 53.8 1.0

P.Soares, M.S.Gadd, J.Frost, C.Galdeano, L.Ellis, O.Epemolu, S.Rocha, K.D.Read, A.Ciulli. Group-Based Optimization of Potent and Cell-Active Inhibitors of the Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3, 3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (VH298). J. Med. Chem. V. 61 599 2018.
ISSN: ISSN 1520-4804
PubMed: 28853884
DOI: 10.1021/ACS.JMEDCHEM.7B00675