Arsenic in PDB 4w9i: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10), PDB code: 4w9i was solved by M.S.Gadd, P.Soares, C.Galdeano, I.Van Molle, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.40 / 2.40
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.402, 93.402, 364.322, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.5

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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) (pdb code 4w9i). 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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10), PDB code: 4w9i:
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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:54.4 occ:1.00 AS A:CAS60 0.0 54.4 1.0 CE2 A:CAS60 2.0 57.4 1.0 CE1 A:CAS60 2.0 58.4 1.0 SG A:CAS60 2.3 42.0 1.0 CB A:CAS60 3.2 35.6 1.0 CA A:CAS60 3.4 34.6 1.0 CD2 A:LEU51 3.8 38.0 1.0 N A:CAS60 4.1 32.9 1.0 O A:GLU59 4.5 33.5 1.0 CB A:LYS55 4.5 31.1 1.0 CG A:LYS55 4.5 33.9 1.0 C A:GLU59 4.5 34.1 1.0 NE2 A:GLN49 4.6 42.8 1.0 C A:CAS60 4.7 34.4 1.0 O A:CAS60 4.9 35.5 1.0 CD A:GLN49 5.0 41.5 1.0

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


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:65.8 occ:1.00 AS A:CAS89 0.0 65.8 1.0 CE2 A:CAS89 2.0 65.6 1.0 CE1 A:CAS89 2.0 66.9 1.0 SG A:CAS89 2.2 54.4 1.0 CB A:CAS89 3.0 50.8 1.0 CA A:CAS89 3.5 45.9 1.0 C A:CAS89 4.0 41.0 1.0 N A:ILE90 4.1 39.3 1.0 OE2 A:GLU91 4.4 59.5 1.0 O A:ILE90 4.6 37.2 1.0 C A:ILE90 4.7 38.1 1.0 N A:CAS89 4.8 45.2 1.0 O A:CAS89 4.9 39.3 1.0 O A:LEU88 5.0 50.0 1.0

Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:47.0 occ:1.00 AS C:CAS77 0.0 47.0 1.0 CE2 C:CAS77 2.0 47.3 1.0 CE1 C:CAS77 2.0 46.0 1.0 SG C:CAS77 2.2 38.6 1.0 CB C:CAS77 3.1 34.9 1.0 CA C:CAS77 3.5 31.2 1.0 CA C:GLY106 4.1 34.8 1.0 O C:THR105 4.2 34.6 1.0 C C:CAS77 4.3 30.5 1.0 N C:GLY106 4.4 35.4 1.0 N C:ASN78 4.4 30.3 1.0 C C:THR105 4.4 35.2 1.0 CZ C:PHE148 4.4 49.4 1.0 CZ K:PHE109 4.6 43.4 1.0 CE K:MET45 4.6 73.1 1.0 CE2 C:PHE148 4.7 49.3 1.0 N C:CAS77 4.7 28.9 1.0 O C:PHE76 4.8 29.3 1.0 CG2 C:ILE75 4.9 33.4 1.0

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


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:54.2 occ:1.00 AS D:CAS60 0.0 54.2 1.0 CE1 D:CAS60 2.0 57.1 1.0 CE2 D:CAS60 2.0 56.1 1.0 SG D:CAS60 2.2 46.4 1.0 CB D:CAS60 3.1 40.2 1.0 CA D:CAS60 3.3 36.8 1.0 N D:CAS60 4.0 35.7 1.0 CD2 D:LEU51 4.2 43.6 1.0 O D:GLU59 4.3 35.3 1.0 C D:GLU59 4.4 35.4 1.0 NE2 D:GLN49 4.5 44.2 1.0 C D:CAS60 4.6 34.7 1.0 CB D:LYS55 4.7 46.5 1.0 CG D:LYS55 4.8 48.3 1.0 O D:CAS60 4.8 34.2 1.0 CD D:GLN49 5.0 43.6 1.0

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


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:98.7 occ:1.00 AS D:CAS89 0.0 98.7 1.0 CE2 D:CAS89 2.0 0.6 1.0 CE1 D:CAS89 2.0 98.0 1.0 SG D:CAS89 2.2 89.6 1.0 CB D:CAS89 3.1 81.6 1.0 CA D:CAS89 3.5 72.7 1.0 N D:ILE90 4.1 64.9 1.0 C D:CAS89 4.1 67.7 1.0 C D:ILE90 4.8 63.5 1.0 O D:ILE90 4.8 62.8 1.0 N D:CAS89 4.9 69.5 1.0 O D:LEU88 5.0 69.0 1.0

Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:47.9 occ:1.00 AS F:CAS77 0.0 47.9 1.0 CE2 F:CAS77 2.0 48.9 1.0 CE1 F:CAS77 2.0 47.4 1.0 SG F:CAS77 2.2 39.8 1.0 CB F:CAS77 3.1 36.3 1.0 CA F:CAS77 3.6 33.2 1.0 CA F:GLY106 4.1 39.7 1.0 O F:THR105 4.1 34.8 1.0 N F:GLY106 4.2 38.9 1.0 C F:THR105 4.3 38.6 1.0 C F:CAS77 4.3 31.6 1.0 N F:ASN78 4.5 30.9 1.0 CE H:MET45 4.5 76.3 1.0 CZ F:PHE148 4.6 49.4 1.0 N F:CAS77 4.8 32.9 1.0 CE2 F:PHE148 4.9 48.8 1.0 O F:PHE76 5.0 33.8 1.0

Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:60.3 occ:1.00 AS G:CAS60 0.0 60.3 1.0 CE1 G:CAS60 2.0 61.5 1.0 CE2 G:CAS60 2.0 61.7 1.0 SG G:CAS60 2.2 54.0 1.0 CB G:CAS60 3.1 49.9 1.0 CA G:CAS60 3.3 48.7 1.0 N G:CAS60 4.0 48.9 1.0 CD2 G:LEU51 4.0 50.3 1.0 NE2 G:GLN49 4.3 50.9 1.0 C G:GLU59 4.5 51.4 1.0 C G:CAS60 4.5 46.8 1.0 O G:GLU59 4.6 51.2 1.0 CB G:LYS55 4.7 58.7 1.0 CD G:GLN49 4.7 50.6 1.0 CG G:LYS55 4.8 60.5 1.0 O G:CAS60 4.8 46.4 1.0 OE1 G:GLN49 4.8 48.9 1.0

Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:85.1 occ:1.00 AS G:CAS89 0.0 85.1 1.0 CE1 G:CAS89 2.0 83.4 1.0 CE2 G:CAS89 2.0 88.0 1.0 SG G:CAS89 2.2 63.0 1.0 CB G:CAS89 3.0 54.7 1.0 CA G:CAS89 3.7 49.2 1.0 C G:CAS89 4.2 43.9 1.0 N G:ILE90 4.3 42.3 1.0 O G:ILE90 4.7 41.7 1.0 O G:HOH214 4.7 41.6 1.0 C G:ILE90 4.9 41.7 1.0

Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10)


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:44.9 occ:1.00 AS I:CAS77 0.0 44.9 1.0 CE2 I:CAS77 2.0 43.6 1.0 CE1 I:CAS77 2.0 46.8 1.0 SG I:CAS77 2.2 35.7 1.0 CB I:CAS77 3.1 32.4 1.0 CA I:CAS77 3.5 29.8 1.0 CA I:GLY106 3.9 31.7 1.0 C I:CAS77 4.1 28.9 1.0 N I:GLY106 4.1 31.8 1.0 O I:THR105 4.1 29.3 1.0 N I:ASN78 4.2 29.1 1.0 C I:THR105 4.2 31.5 1.0 N I:CAS77 4.8 29.1 1.0 CE2 I:PHE148 4.9 42.8 1.0 O I:CAS77 4.9 28.2 1.0 O I:PHE76 5.0 30.7 1.0

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


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-((2S,4R)-1-Acetyl-4- Hydroxypyrrolidine-2-Carbonyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 10) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:60.7 occ:1.00 AS J:CAS60 0.0 60.7 1.0 CE2 J:CAS60 2.0 60.6 1.0 CE1 J:CAS60 2.0 59.9 1.0 SG J:CAS60 2.3 46.7 1.0 CB J:CAS60 3.2 39.5 1.0 CA J:CAS60 3.4 37.5 1.0 N J:CAS60 4.1 35.7 1.0 CD2 J:LEU51 4.1 36.4 1.0 O J:GLU59 4.4 38.2 1.0 C J:GLU59 4.5 37.9 1.0 NE2 J:GLN49 4.5 40.5 1.0 CB J:LYS55 4.6 35.4 1.0 C J:CAS60 4.6 35.4 1.0 CG J:LYS55 4.7 37.3 1.0 O J:CAS60 4.8 34.4 1.0 CD J:GLN49 5.0 38.5 1.0

C.Galdeano, M.S.Gadd, P.Soares, S.Scaffidi, I.Van Molle, I.Birced, S.Hewitt, D.M.Dias, A.Ciulli. Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction Between the Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (Hif) Alpha Subunit with in Vitro Nanomolar Affinities. J.Med.Chem. V. 57 8657 2014.
ISSN: ISSN 0022-2623
PubMed: 25166285
DOI: 10.1021/JM5011258