Arsenic in PDB 4w9k: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-3- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-((S)-2-Acetamido-3- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14), PDB code: 4w9k 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)	93.70 / 2.10
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.696, 93.696, 361.740, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 26

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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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) (pdb code 4w9k). 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14), PDB code: 4w9k:
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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:54.3 occ:1.00 AS A:CAS60 0.0 54.3 1.0 CE1 A:CAS60 2.0 57.6 1.0 CE2 A:CAS60 2.0 55.5 1.0 SG A:CAS60 2.3 38.3 1.0 CB A:CAS60 3.2 33.9 1.0 CA A:CAS60 3.4 31.2 1.0 CD2 A:LEU51 3.8 33.3 1.0 N A:CAS60 4.0 29.0 1.0 CG A:LYS55 4.5 36.7 1.0 O A:GLU59 4.5 29.9 1.0 CB A:LYS55 4.5 32.9 1.0 C A:GLU59 4.5 29.9 1.0 C A:CAS60 4.6 30.8 1.0 NE2 A:GLN49 4.7 41.0 1.0 O A:CAS60 4.9 31.3 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:82.2 occ:1.00 AS A:CAS89 0.0 82.2 1.0 CE1 A:CAS89 2.0 86.9 1.0 CE2 A:CAS89 2.0 84.7 1.0 SG A:CAS89 2.2 61.3 1.0 CB A:CAS89 3.1 54.6 1.0 CA A:CAS89 3.6 48.9 1.0 C A:CAS89 4.0 44.8 1.0 N A:ILE90 4.0 44.4 1.0 OE2 A:GLU91 4.2 71.3 1.0 O A:HOH240 4.4 53.0 1.0 O A:ILE90 4.5 43.5 1.0 C A:ILE90 4.7 42.8 1.0 O A:CAS89 4.8 41.7 1.0 CA A:ILE90 5.0 42.6 1.0 N A:CAS89 5.0 46.2 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:64.2 occ:1.00 AS C:CAS77 0.0 64.2 1.0 CE1 C:CAS77 2.0 60.6 1.0 CE2 C:CAS77 2.0 64.9 1.0 SG C:CAS77 2.2 53.7 1.0 CB C:CAS77 3.1 47.7 1.0 CA C:CAS77 3.5 42.9 1.0 CA C:GLY106 4.1 43.6 1.0 O C:THR105 4.2 46.3 1.0 C C:CAS77 4.3 42.2 1.0 CE2 C:PHE148 4.4 65.3 1.0 N C:GLY106 4.4 45.1 1.0 C C:THR105 4.4 47.0 1.0 N C:ASN78 4.5 40.7 1.0 CE K:MET45 4.5 81.6 1.0 CZ K:PHE109 4.6 49.3 1.0 CZ C:PHE148 4.7 68.8 1.0 N C:CAS77 4.8 41.5 1.0 O C:PHE76 4.9 38.0 1.0 CG2 C:ILE75 4.9 44.1 1.0 O C:GLY104 4.9 56.3 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:58.3 occ:1.00 AS D:CAS60 0.0 58.3 1.0 CE1 D:CAS60 2.0 61.9 1.0 CE2 D:CAS60 2.0 64.1 1.0 SG D:CAS60 2.2 48.6 1.0 CB D:CAS60 3.1 43.2 1.0 CA D:CAS60 3.4 38.7 1.0 N D:CAS60 4.0 37.4 1.0 CD2 D:LEU51 4.1 48.0 1.0 NE2 D:GLN49 4.2 44.7 1.0 O D:GLU59 4.4 39.2 1.0 C D:GLU59 4.5 37.0 1.0 C D:CAS60 4.6 39.6 1.0 CB D:LYS55 4.7 51.3 1.0 CD D:GLN49 4.7 44.6 1.0 CG D:LYS55 4.7 53.9 1.0 O D:CAS60 4.8 41.0 1.0 OE1 D:GLN49 5.0 42.4 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) 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 CE1 D:CAS89 2.0 0.7 1.0 CE2 D:CAS89 2.0 0.8 1.0 SG D:CAS89 2.2 97.2 1.0 CB D:CAS89 3.1 89.3 1.0 CA D:CAS89 3.6 77.8 1.0 N D:ILE90 4.0 68.2 1.0 C D:CAS89 4.1 70.8 1.0 O D:ILE90 4.7 61.0 1.0 C D:ILE90 4.8 61.4 1.0 N D:CAS89 5.0 73.4 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:73.1 occ:1.00 AS F:CAS77 0.0 73.1 1.0 CE1 F:CAS77 2.0 71.1 1.0 CE2 F:CAS77 2.0 72.3 1.0 SG F:CAS77 2.2 61.3 1.0 CB F:CAS77 3.1 56.2 1.0 CA F:CAS77 3.5 50.8 1.0 CA F:GLY106 4.0 57.1 1.0 O F:THR105 4.3 48.9 1.0 C F:CAS77 4.3 47.8 1.0 N F:GLY106 4.3 54.6 1.0 C F:THR105 4.4 53.2 1.0 CE H:MET45 4.5 91.6 1.0 N F:ASN78 4.5 46.2 1.0 CE2 F:PHE148 4.5 75.5 1.0 N F:CAS77 4.8 50.9 1.0 CZ F:PHE148 4.8 80.3 1.0 CG2 F:ILE75 4.9 62.8 1.0 O F:GLY104 4.9 59.9 1.0 NH2 F:ARG79 5.0 69.7 1.0 O F:PHE76 5.0 56.5 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:71.0 occ:1.00 AS G:CAS60 0.0 71.0 1.0 CE1 G:CAS60 2.0 68.5 1.0 CE2 G:CAS60 2.0 72.8 1.0 SG G:CAS60 2.2 61.4 1.0 CB G:CAS60 3.2 55.6 1.0 CA G:CAS60 3.3 54.3 1.0 CD2 G:LEU51 4.0 54.8 1.0 NE2 G:GLN49 4.0 51.4 1.0 N G:CAS60 4.1 52.2 1.0 CD G:GLN49 4.5 49.5 1.0 C G:CAS60 4.5 53.8 1.0 C G:GLU59 4.6 54.3 1.0 O G:GLU59 4.6 56.3 1.0 OE1 G:GLN49 4.7 51.3 1.0 O G:CAS60 4.7 54.9 1.0 CB G:LYS55 4.7 59.8 1.0 CG G:LYS55 4.8 61.7 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.2 occ:1.00 AS G:CAS89 0.0 0.2 1.0 CE1 G:CAS89 2.0 97.7 1.0 CE2 G:CAS89 2.0 0.9 1.0 SG G:CAS89 2.2 75.9 1.0 CB G:CAS89 3.1 60.2 1.0 CA G:CAS89 3.6 54.0 1.0 N G:ILE90 4.1 45.0 1.0 C G:CAS89 4.2 48.4 1.0 O G:HOH213 4.4 51.4 1.0 O G:ILE90 4.6 44.6 1.0 C G:ILE90 4.8 44.9 1.0 N G:CAS89 5.0 53.8 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:55.6 occ:1.00 AS I:CAS77 0.0 55.6 1.0 CE2 I:CAS77 2.0 51.1 1.0 CE1 I:CAS77 2.0 57.7 1.0 SG I:CAS77 2.2 46.7 1.0 CB I:CAS77 3.1 40.6 1.0 CA I:CAS77 3.5 37.0 1.0 CA I:GLY106 3.9 41.9 1.0 N I:GLY106 4.0 42.6 1.0 O I:THR105 4.1 39.7 1.0 C I:CAS77 4.1 36.0 1.0 C I:THR105 4.2 43.0 1.0 N I:ASN78 4.2 34.6 1.0 N I:CAS77 4.8 38.2 1.0 O I:GLY104 4.9 46.3 1.0 O I:CAS77 4.9 37.5 1.0 CE2 I:PHE148 4.9 46.6 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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14)


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- Phenylpropanamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4- Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 14) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:66.6 occ:1.00 AS J:CAS60 0.0 66.6 1.0 CE2 J:CAS60 2.0 67.9 1.0 CE1 J:CAS60 2.0 69.5 1.0 SG J:CAS60 2.3 47.3 1.0 CB J:CAS60 3.2 39.2 1.0 CA J:CAS60 3.4 36.5 1.0 CD2 J:LEU51 3.9 36.3 1.0 N J:CAS60 4.0 32.8 1.0 O J:GLU59 4.4 37.3 1.0 C J:GLU59 4.5 35.6 1.0 CG J:LYS55 4.5 40.1 1.0 NE2 J:GLN49 4.5 39.7 1.0 CB J:LYS55 4.6 37.3 1.0 C J:CAS60 4.6 36.7 1.0 O J:CAS60 4.9 33.8 1.0 CD J:GLN49 4.9 38.0 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