Arsenic in PDB 4w9j: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13), PDB code: 4w9j was solved by M.S.Gadd, 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)	93.71 / 2.20
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.708, 93.708, 360.836, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 26.5

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>>> 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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) (pdb code 4w9j). 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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13), PDB code: 4w9j:
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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:45.8 occ:1.00 AS A:CAS60 0.0 45.8 1.0 CE2 A:CAS60 2.0 49.5 1.0 CE1 A:CAS60 2.0 48.6 1.0 SG A:CAS60 2.3 33.5 1.0 CB A:CAS60 3.2 29.1 1.0 CA A:CAS60 3.4 27.3 1.0 CD2 A:LEU51 3.7 27.6 1.0 N A:CAS60 4.0 26.1 1.0 CB A:LYS55 4.5 27.6 1.0 CG A:LYS55 4.5 30.1 1.0 O A:GLU59 4.5 27.7 1.0 NE2 A:GLN49 4.5 36.0 1.0 C A:GLU59 4.5 27.9 1.0 C A:CAS60 4.7 27.1 1.0 CG A:LEU51 5.0 26.7 1.0 O A:CAS60 5.0 26.5 1.0 CD A:GLN49 5.0 35.7 1.0

Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:58.9 occ:1.00 AS A:CAS89 0.0 58.9 1.0 CE1 A:CAS89 2.0 62.2 1.0 CE2 A:CAS89 2.0 63.0 1.0 SG A:CAS89 2.2 45.6 1.0 CB A:CAS89 3.1 41.2 1.0 CA A:CAS89 3.7 37.2 1.0 OE2 A:GLU91 3.9 59.5 1.0 N A:ILE90 4.1 34.6 1.0 O A:HOH250 4.2 39.1 1.0 C A:CAS89 4.2 34.4 1.0 O A:HOH245 4.3 34.5 1.0 O A:ILE90 4.6 32.1 1.0 C A:ILE90 4.7 33.1 1.0 O A:HOH255 4.8 48.1 1.0 CD A:GLU91 4.9 54.3 1.0

Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:50.3 occ:1.00 AS C:CAS77 0.0 50.3 1.0 CE1 C:CAS77 2.0 50.3 1.0 CE2 C:CAS77 2.0 53.0 1.0 SG C:CAS77 2.2 41.4 1.0 CB C:CAS77 3.1 34.4 1.0 CA C:CAS77 3.5 30.9 1.0 CA C:GLY106 4.2 33.0 1.0 C C:CAS77 4.2 30.6 1.0 CE K:MET45 4.3 79.6 1.0 O C:THR105 4.3 30.9 1.0 N C:GLY106 4.4 32.8 1.0 N C:ASN78 4.5 30.0 1.0 CE2 C:PHE148 4.5 53.4 1.0 C C:THR105 4.5 33.2 1.0 CZ C:PHE148 4.5 55.3 1.0 N C:CAS77 4.8 29.4 1.0 O C:PHE76 5.0 28.9 1.0

Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:52.4 occ:1.00 AS D:CAS60 0.0 52.4 1.0 CE2 D:CAS60 2.0 54.6 1.0 CE1 D:CAS60 2.0 55.5 1.0 SG D:CAS60 2.3 46.0 1.0 CB D:CAS60 3.2 39.4 1.0 CA D:CAS60 3.4 36.4 1.0 N D:CAS60 4.1 34.8 1.0 CD2 D:LEU51 4.2 43.5 1.0 O D:GLU59 4.3 35.0 1.0 NE2 D:GLN49 4.3 42.3 1.0 C D:GLU59 4.5 34.5 1.0 C D:CAS60 4.6 34.7 1.0 CD D:GLN49 4.8 42.1 1.0 CB D:LYS55 4.9 44.4 1.0 CG D:LYS55 4.9 46.4 1.0 O D:CAS60 4.9 34.9 1.0

Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:95.0 occ:1.00 AS D:CAS89 0.0 95.0 1.0 CE1 D:CAS89 2.0 92.3 1.0 CE2 D:CAS89 2.0 97.4 1.0 SG D:CAS89 2.2 78.5 1.0 CB D:CAS89 3.2 72.4 1.0 CA D:CAS89 3.7 65.6 1.0 N D:ILE90 4.1 57.4 1.0 C D:CAS89 4.1 60.4 1.0 O D:HOH227 4.6 64.1 1.0 C D:ILE90 4.7 53.3 1.0 O D:ILE90 4.7 50.4 1.0 O D:CAS89 4.9 59.3 1.0 N D:GLU91 5.0 56.0 1.0

Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:55.4 occ:1.00 AS F:CAS77 0.0 55.4 1.0 CE1 F:CAS77 2.0 52.7 1.0 CE2 F:CAS77 2.0 53.5 1.0 SG F:CAS77 2.2 44.3 1.0 CB F:CAS77 3.1 38.6 1.0 CA F:CAS77 3.5 35.0 1.0 CA F:GLY106 4.0 38.7 1.0 N F:GLY106 4.2 39.0 1.0 O F:THR105 4.2 36.4 1.0 C F:CAS77 4.3 33.0 1.0 C F:THR105 4.3 38.8 1.0 N F:ASN78 4.5 32.4 1.0 CE2 F:PHE148 4.5 51.2 1.0 CE H:MET45 4.8 91.2 1.0 N F:CAS77 4.8 35.5 1.0 CZ F:PHE148 4.8 52.5 1.0 O F:GLY104 4.9 46.8 1.0 CG2 F:ILE75 4.9 41.5 1.0 CZ H:PHE109 5.0 57.1 1.0 O F:PHE76 5.0 37.0 1.0

Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:73.7 occ:1.00 AS G:CAS60 0.0 73.7 1.0 CE2 G:CAS60 2.0 74.3 1.0 CE1 G:CAS60 2.0 71.3 1.0 SG G:CAS60 2.2 66.2 1.0 CB G:CAS60 3.2 61.7 1.0 CA G:CAS60 3.4 60.0 1.0 NE2 G:GLN49 4.0 59.9 1.0 N G:CAS60 4.0 58.7 1.0 CD2 G:LEU51 4.1 56.1 1.0 C G:CAS60 4.6 58.8 1.0 C G:GLU59 4.6 58.5 1.0 O G:GLU59 4.6 59.9 1.0 CD G:GLN49 4.6 58.6 1.0 O G:CAS60 4.8 58.9 1.0 CB G:LYS55 4.8 61.8 1.0 OE1 G:GLN49 4.9 59.5 1.0 CG G:LYS55 4.9 63.8 1.0

Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:98.3 occ:1.00 AS G:CAS89 0.0 98.3 1.0 CE1 G:CAS89 2.0 94.1 1.0 CE2 G:CAS89 2.0 99.1 1.0 SG G:CAS89 2.2 71.8 1.0 CB G:CAS89 3.0 63.5 1.0 CA G:CAS89 3.6 56.6 1.0 N G:ILE90 4.2 50.0 1.0 O G:HOH214 4.2 43.4 1.0 C G:CAS89 4.2 51.2 1.0 O G:ILE90 4.8 48.2 1.0 N G:CAS89 4.9 54.1 1.0 O G:LEU88 4.9 53.2 1.0 C G:ILE90 5.0 46.9 1.0

Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:44.6 occ:1.00 AS I:CAS77 0.0 44.6 1.0 CE1 I:CAS77 2.0 44.8 1.0 CE2 I:CAS77 2.0 41.2 1.0 SG I:CAS77 2.2 34.3 1.0 CB I:CAS77 3.2 28.2 1.0 CA I:CAS77 3.5 26.2 1.0 CA I:GLY106 3.9 27.5 1.0 N I:GLY106 4.1 28.4 1.0 O I:THR105 4.1 28.8 1.0 C I:CAS77 4.1 25.8 1.0 C I:THR105 4.2 29.5 1.0 N I:ASN78 4.3 25.6 1.0 N I:CAS77 4.8 24.6 1.0 CE2 I:PHE148 4.9 32.1 1.0 O I:CAS77 5.0 25.9 1.0 O I:PHE76 5.0 27.9 1.0

Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13)


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-((S)-2-Acetamido-4- Methylpentanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 13) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:62.9 occ:1.00 AS J:CAS60 0.0 62.9 1.0 CE2 J:CAS60 2.0 62.9 1.0 CE1 J:CAS60 2.0 63.0 1.0 SG J:CAS60 2.2 43.4 1.0 CB J:CAS60 3.2 37.9 1.0 CA J:CAS60 3.4 36.2 1.0 CD2 J:LEU51 4.0 35.3 1.0 N J:CAS60 4.1 34.5 1.0 NE2 J:GLN49 4.3 36.6 1.0 O J:GLU59 4.4 36.2 1.0 C J:GLU59 4.5 36.4 1.0 C J:CAS60 4.6 36.4 1.0 CG J:LYS55 4.7 41.5 1.0 CB J:LYS55 4.7 38.1 1.0 CD J:GLN49 4.8 35.1 1.0 O J:CAS60 4.9 35.7 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