Arsenic in PDB 4w9h: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7), PDB code: 4w9h 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)	93.10 / 2.10
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.980, 92.980, 364.372, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) (pdb code 4w9h). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 14 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7), PDB code: 4w9h:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:53.2 occ:1.00 AS A:CAS60 0.0 53.2 1.0 CE1 A:CAS60 2.0 53.2 1.0 CE2 A:CAS60 2.0 50.8 1.0 SG A:CAS60 2.3 39.2 1.0 CB A:CAS60 3.1 33.3 1.0 CA A:CAS60 3.5 31.0 1.0 CD2 A:LEU51 3.6 34.8 1.0 N A:CAS60 4.2 29.6 1.0 NE2 A:GLN49 4.4 43.9 1.0 CB A:LYS55 4.4 30.5 1.0 CG A:LYS55 4.5 34.4 1.0 O A:GLU59 4.6 32.1 1.0 C A:GLU59 4.7 31.6 1.0 C A:CAS60 4.7 32.4 1.0 CA A:LEU51 4.8 37.1 1.0 CG A:LEU51 4.8 35.8 1.0 CD A:GLN49 4.8 42.4 1.0 CB A:LEU51 4.8 36.0 1.0 O A:CAS60 4.9 32.4 1.0

Arsenic binding site 2 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:74.5 occ:1.00 AS A:CAS89 0.0 74.5 1.0 CE2 A:CAS89 2.0 75.8 1.0 CE1 A:CAS89 2.0 75.7 1.0 SG A:CAS89 2.2 61.0 1.0 CB A:CAS89 3.1 51.1 1.0 CA A:CAS89 3.6 46.1 1.0 N A:ILE90 4.0 41.6 1.0 C A:CAS89 4.0 42.5 1.0 OE2 A:GLU91 4.3 60.3 1.0 O A:ILE90 4.6 40.8 1.0 C A:ILE90 4.7 40.8 1.0 O A:CAS89 4.9 40.5 1.0 N A:CAS89 4.9 43.5 1.0

Arsenic binding site 3 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ B:As112 b:96.3 occ:1.00 AS B:CAS112 0.0 96.3 1.0 CE2 B:CAS112 2.0 87.8 1.0 CE1 B:CAS112 2.0 88.7 1.0 SG B:CAS112 2.2 64.3 1.0 CB B:CAS112 2.7 61.8 1.0 CE1 B:PHE77 3.5 42.1 1.0 CB B:SER39 4.0 41.4 1.0 CA B:CAS112 4.1 54.9 1.0 CZ B:PHE77 4.3 42.5 1.0 CD1 B:PHE77 4.3 39.3 1.0 CB B:LEU110 4.3 37.8 1.0 CA B:SER39 4.5 43.7 1.0 N B:CAS112 4.6 50.1 1.0 O B:LEU110 4.6 40.8 1.0 C B:CAS112 4.6 50.4 1.0 N B:SER39 4.7 47.4 1.0 OG B:SER39 4.7 42.3 1.0 O B:CAS112 4.7 50.9 1.0 CG2 B:THR38 4.8 61.5 1.0 CG1 B:VAL73 4.8 30.2 1.0 CD2 B:TYR76 4.9 33.1 1.0 CD1 B:LEU110 4.9 37.7 1.0 C B:LEU110 5.0 40.2 1.0

Arsenic binding site 4 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:52.3 occ:1.00 AS C:CAS77 0.0 52.3 1.0 CE1 C:CAS77 2.0 56.1 1.0 CE2 C:CAS77 2.0 54.4 1.0 SG C:CAS77 2.2 41.5 1.0 CB C:CAS77 3.0 37.8 1.0 CA C:CAS77 3.6 34.0 1.0 CE K:MET45 4.0 81.1 1.0 CZ C:PHE148 4.1 55.8 1.0 CA C:GLY106 4.2 44.9 1.0 O C:THR105 4.3 39.5 1.0 C C:CAS77 4.4 33.6 1.0 N C:GLY106 4.5 43.7 1.0 C C:THR105 4.5 42.5 1.0 N C:ASN78 4.6 32.9 1.0 CZ K:PHE109 4.7 59.2 1.0 CE2 C:PHE148 4.7 58.5 1.0 N C:CAS77 4.8 31.5 1.0 SD K:MET45 4.9 77.8 1.0 CG K:MET45 4.9 69.0 1.0 CG2 C:ILE75 4.9 38.0 1.0 NH2 C:ARG79 5.0 68.2 1.0 O C:PHE76 5.0 30.8 1.0

Arsenic binding site 5 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:52.7 occ:1.00 AS D:CAS60 0.0 52.7 1.0 CE1 D:CAS60 2.0 55.5 1.0 CE2 D:CAS60 2.0 58.9 1.0 SG D:CAS60 2.2 44.4 1.0 CB D:CAS60 3.1 37.5 1.0 CA D:CAS60 3.4 33.5 1.0 N D:CAS60 4.1 31.6 1.0 CD2 D:LEU51 4.1 39.1 1.0 NE2 D:GLN49 4.3 36.4 1.0 O D:GLU59 4.5 31.9 1.0 C D:GLU59 4.5 31.8 1.0 CG D:LYS55 4.6 46.1 1.0 CB D:LYS55 4.6 43.1 1.0 C D:CAS60 4.6 31.9 1.0 CD D:GLN49 4.8 36.0 1.0 O D:CAS60 4.9 31.7 1.0

Arsenic binding site 6 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:92.4 occ:1.00 AS D:CAS89 0.0 92.4 1.0 CE1 D:CAS89 2.0 90.4 1.0 CE2 D:CAS89 2.0 94.3 1.0 SG D:CAS89 2.2 82.9 1.0 CB D:CAS89 3.1 66.6 1.0 CA D:CAS89 3.6 58.6 1.0 N D:ILE90 4.1 52.0 1.0 C D:CAS89 4.1 53.5 1.0 O D:ILE90 4.8 48.8 1.0 C D:ILE90 4.8 47.9 1.0 N D:CAS89 5.0 55.4 1.0 O D:CAS89 5.0 51.6 1.0

Arsenic binding site 7 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ E:As112 b:92.6 occ:1.00 AS E:CAS112 0.0 92.6 1.0 CE1 E:CAS112 2.0 90.2 1.0 CE2 E:CAS112 2.0 86.1 1.0 SG E:CAS112 2.2 58.5 1.0 CB E:CAS112 2.8 50.1 1.0 CE1 E:PHE77 3.4 45.0 1.0 CG1 E:VAL73 4.2 29.4 1.0 CZ E:PHE77 4.2 43.5 1.0 CB E:LEU110 4.2 34.8 1.0 CA E:CAS112 4.2 42.3 1.0 CD1 E:PHE77 4.3 42.6 1.0 CB E:SER39 4.3 44.1 1.0 CD1 E:LEU110 4.5 36.1 1.0 N E:CAS112 4.7 36.0 1.0 C E:CAS112 4.7 40.5 1.0 CD2 F:LEU158 4.7 32.9 1.0 CD2 E:TYR76 4.8 27.9 1.0 O E:CAS112 4.8 41.6 1.0 OG E:SER39 4.9 41.6 1.0 CG E:LEU110 5.0 35.7 1.0 O E:LEU110 5.0 34.0 1.0

Arsenic binding site 8 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:47.1 occ:1.00 AS F:CAS77 0.0 47.1 1.0 CE1 F:CAS77 2.0 49.9 1.0 CE2 F:CAS77 2.0 50.4 1.0 SG F:CAS77 2.2 37.2 1.0 CB F:CAS77 3.1 33.1 1.0 CA F:CAS77 3.6 29.9 1.0 CA F:GLY106 4.1 38.2 1.0 CE H:MET45 4.1 50.8 1.0 O F:THR105 4.1 32.5 1.0 CZ F:PHE148 4.2 48.5 1.0 N F:GLY106 4.3 35.4 1.0 C F:THR105 4.3 36.6 1.0 C F:CAS77 4.4 29.5 1.0 N F:ASN78 4.6 28.8 1.0 CG H:MET45 4.7 50.4 1.0 NH1 F:ARG79 4.8 63.8 1.0 SD H:MET45 4.8 50.9 1.0 N F:CAS77 4.8 29.6 1.0 CE1 F:PHE148 4.9 45.6 1.0

Arsenic binding site 9 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:50.8 occ:1.00 AS G:CAS60 0.0 50.8 1.0 CE1 G:CAS60 2.0 50.3 1.0 CE2 G:CAS60 2.0 52.5 1.0 SG G:CAS60 2.2 43.5 1.0 CB G:CAS60 3.1 39.7 1.0 CA G:CAS60 3.4 38.4 1.0 CD2 G:LEU51 3.8 36.8 1.0 N G:CAS60 4.1 38.4 1.0 NE2 G:GLN49 4.2 35.8 1.0 CD G:GLN49 4.6 33.8 1.0 C G:CAS60 4.6 37.4 1.0 O G:GLU59 4.6 40.4 1.0 C G:GLU59 4.6 40.2 1.0 CB G:LYS55 4.8 45.9 1.0 CG G:LYS55 4.8 47.8 1.0 O G:CAS60 4.8 39.2 1.0 OE1 G:GLN49 4.9 31.9 1.0

Arsenic binding site 10 out of 14 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7)


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-Acetamido-3,3- Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 7) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:74.9 occ:1.00 AS G:CAS89 0.0 74.9 1.0 CE1 G:CAS89 2.0 74.7 1.0 CE2 G:CAS89 2.0 78.9 1.0 SG G:CAS89 2.2 54.8 1.0 CB G:CAS89 2.9 42.9 1.0 CA G:CAS89 3.5 37.6 1.0 O G:HOH251 3.8 48.5 1.0 C G:CAS89 4.1 33.5 1.0 N G:ILE90 4.1 32.0 1.0 O G:HOH222 4.6 39.8 1.0 O G:ILE90 4.7 31.5 1.0 N G:CAS89 4.9 35.5 1.0 C G:ILE90 4.9 32.0 1.0 O G:CAS89 5.0 32.4 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