Arsenic in PDB 4w9l: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15), PDB code: 4w9l 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)	93.82 / 2.20
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.825, 93.825, 362.612, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 24.3

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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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) (pdb code 4w9l). 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15), PDB code: 4w9l:
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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:70.5 occ:1.00 AS A:CAS60 0.0 70.5 1.0 CE2 A:CAS60 2.0 68.3 1.0 CE1 A:CAS60 2.0 69.5 1.0 SG A:CAS60 2.3 46.0 1.0 CB A:CAS60 3.3 39.1 1.0 CA A:CAS60 3.4 36.9 1.0 CD2 A:LEU51 3.7 37.2 1.0 N A:CAS60 4.1 35.8 1.0 CG A:LYS55 4.3 40.4 1.0 CB A:LYS55 4.4 36.6 1.0 O A:GLU59 4.4 37.1 1.0 C A:GLU59 4.5 37.5 1.0 C A:CAS60 4.7 36.2 1.0 CG A:LEU51 4.9 36.5 1.0 O A:CAS60 4.9 35.6 1.0 CB A:LEU51 5.0 36.5 1.0 CA A:LEU51 5.0 38.5 1.0 NE2 A:GLN49 5.0 46.0 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:91.3 occ:1.00 AS A:CAS89 0.0 91.3 1.0 CE2 A:CAS89 2.0 91.4 1.0 CE1 A:CAS89 2.0 92.1 1.0 SG A:CAS89 2.2 70.6 1.0 CB A:CAS89 3.2 56.6 1.0 CA A:CAS89 3.6 48.3 1.0 N A:ILE90 3.9 43.1 1.0 C A:CAS89 4.0 44.3 1.0 OE2 A:GLU91 4.2 83.8 1.0 O A:ILE90 4.6 45.9 1.0 C A:ILE90 4.6 44.5 1.0 O A:CAS89 4.9 41.1 1.0 CA A:ILE90 4.9 43.3 1.0 N A:CAS89 4.9 45.2 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:67.7 occ:1.00 AS C:CAS77 0.0 67.7 1.0 CE1 C:CAS77 2.0 68.7 1.0 CE2 C:CAS77 2.0 69.7 1.0 SG C:CAS77 2.2 52.2 1.0 CB C:CAS77 3.1 41.4 1.0 CA C:CAS77 3.6 35.2 1.0 CE K:MET45 4.0 85.1 1.0 CA C:GLY106 4.3 38.6 1.0 C C:CAS77 4.3 34.6 1.0 CE2 C:PHE148 4.4 69.5 1.0 N C:GLY106 4.5 38.2 1.0 O C:THR105 4.5 38.6 1.0 N C:ASN78 4.6 34.2 1.0 CZ C:PHE148 4.6 73.2 1.0 C C:THR105 4.6 39.9 1.0 N C:CAS77 4.9 34.0 1.0 CZ K:PHE109 4.9 46.8 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:70.8 occ:1.00 AS D:CAS60 0.0 70.8 1.0 CE1 D:CAS60 2.0 75.2 1.0 CE2 D:CAS60 2.0 70.3 1.0 SG D:CAS60 2.3 52.3 1.0 CB D:CAS60 3.2 44.8 1.0 CA D:CAS60 3.4 40.5 1.0 CD2 D:LEU51 4.1 49.2 1.0 N D:CAS60 4.1 39.7 1.0 O D:GLU59 4.3 43.4 1.0 NE2 D:GLN49 4.4 52.2 1.0 C D:GLU59 4.5 41.6 1.0 C D:CAS60 4.7 38.7 1.0 CB D:LYS55 4.8 51.6 1.0 CG D:LYS55 4.8 55.2 1.0 O D:CAS60 4.9 39.5 1.0 CD D:GLN49 5.0 50.1 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.1 occ:1.00 AS D:CAS89 0.0 0.1 1.0 CE2 D:CAS89 2.0 0.2 1.0 CE1 D:CAS89 2.0 0.8 1.0 SG D:CAS89 2.2 98.9 1.0 CB D:CAS89 3.2 85.8 1.0 CA D:CAS89 3.6 73.5 1.0 C D:CAS89 4.1 66.7 1.0 N D:ILE90 4.2 63.7 1.0 O D:ILE90 4.6 60.2 1.0 C D:ILE90 4.8 60.3 1.0 O D:HOH208 4.9 68.3 1.0 N D:CAS89 4.9 69.1 1.0 O D:LEU88 5.0 70.2 1.0 O D:CAS89 5.0 63.1 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:74.0 occ:1.00 AS F:CAS77 0.0 74.0 1.0 CE1 F:CAS77 2.0 69.0 1.0 CE2 F:CAS77 2.0 71.9 1.0 SG F:CAS77 2.2 55.9 1.0 CB F:CAS77 3.1 45.8 1.0 CA F:CAS77 3.6 40.1 1.0 CA F:GLY106 4.2 45.0 1.0 CE H:MET45 4.3 0.8 1.0 C F:CAS77 4.4 37.6 1.0 N F:GLY106 4.4 44.6 1.0 O F:THR105 4.4 43.2 1.0 CE2 F:PHE148 4.5 65.3 1.0 C F:THR105 4.5 45.5 1.0 N F:ASN78 4.6 36.8 1.0 CZ F:PHE148 4.8 67.9 1.0 CZ H:PHE109 4.9 65.4 1.0 N F:CAS77 4.9 39.4 1.0 CG2 F:ILE75 5.0 51.2 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:92.6 occ:1.00 AS G:CAS60 0.0 92.6 1.0 CE1 G:CAS60 2.0 91.0 1.0 CE2 G:CAS60 2.0 90.6 1.0 SG G:CAS60 2.2 79.1 1.0 CB G:CAS60 3.2 70.4 1.0 CA G:CAS60 3.4 65.2 1.0 N G:CAS60 4.0 62.6 1.0 CD2 G:LEU51 4.0 60.0 1.0 NE2 G:GLN49 4.2 64.2 1.0 C G:GLU59 4.5 62.6 1.0 O G:GLU59 4.5 64.0 1.0 CB G:LYS55 4.6 64.6 1.0 C G:CAS60 4.6 62.2 1.0 CG G:LYS55 4.7 66.5 1.0 CD G:GLN49 4.7 62.8 1.0 O G:CAS60 4.9 61.8 1.0 OE1 G:GLN49 5.0 62.6 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.6 occ:1.00 AS G:CAS89 0.0 0.6 1.0 CE2 G:CAS89 2.0 0.7 1.0 CE1 G:CAS89 2.0 0.7 1.0 SG G:CAS89 2.2 0.0 1.0 CB G:CAS89 3.1 79.3 1.0 CA G:CAS89 3.9 68.2 1.0 N G:ILE90 4.5 58.5 1.0 C G:CAS89 4.5 61.7 1.0 O G:HOH208 4.8 52.4 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:61.2 occ:1.00 AS I:CAS77 0.0 61.2 1.0 CE1 I:CAS77 2.0 63.4 1.0 CE2 I:CAS77 2.0 60.2 1.0 SG I:CAS77 2.2 46.4 1.0 CB I:CAS77 3.1 37.4 1.0 CA I:CAS77 3.5 33.7 1.0 CA I:GLY106 4.0 36.2 1.0 O I:THR105 4.0 36.0 1.0 C I:CAS77 4.1 32.3 1.0 N I:GLY106 4.1 36.6 1.0 C I:THR105 4.2 36.8 1.0 N I:ASN78 4.3 31.8 1.0 N I:CAS77 4.8 33.1 1.0 CE2 I:PHE148 4.9 46.2 1.0 O I:CAS77 4.9 32.1 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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15)


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-3,3- Dimethylbutanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 15) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:80.2 occ:1.00 AS J:CAS60 0.0 80.2 1.0 CE1 J:CAS60 2.0 82.8 1.0 CE2 J:CAS60 2.0 78.0 1.0 SG J:CAS60 2.3 55.6 1.0 CB J:CAS60 3.3 46.8 1.0 CA J:CAS60 3.5 42.8 1.0 CD2 J:LEU51 4.0 41.7 1.0 N J:CAS60 4.1 41.2 1.0 O J:GLU59 4.4 41.6 1.0 NE2 J:GLN49 4.5 41.8 1.0 CG J:LYS55 4.5 45.2 1.0 C J:GLU59 4.5 42.1 1.0 CB J:LYS55 4.6 42.7 1.0 C J:CAS60 4.7 41.3 1.0 CD J:GLN49 4.9 40.8 1.0 O J:CAS60 4.9 41.5 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