Arsenic in PDB 4w9g: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6), PDB code: 4w9g 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)	93.49 / 2.70
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.487, 93.487, 363.891, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 26.4

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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) (pdb code 4w9g). 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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6), PDB code: 4w9g:
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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6)


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:56.0 occ:1.00 AS A:CAS60 0.0 56.0 1.0 CE2 A:CAS60 2.0 54.2 1.0 CE1 A:CAS60 2.0 56.1 1.0 SG A:CAS60 2.3 43.2 1.0 CB A:CAS60 3.2 37.4 1.0 CA A:CAS60 3.4 35.4 1.0 CD2 A:LEU51 3.9 32.7 1.0 N A:CAS60 4.0 33.9 1.0 O A:GLU59 4.3 36.0 1.0 C A:GLU59 4.4 35.3 1.0 CB A:LYS55 4.5 33.3 1.0 NE2 A:GLN49 4.6 37.8 1.0 CG A:LYS55 4.6 36.1 1.0 C A:CAS60 4.7 34.1 1.0 O A:CAS60 5.0 33.2 1.0

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


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:78.7 occ:1.00 AS A:CAS89 0.0 78.7 1.0 CE2 A:CAS89 2.0 81.4 1.0 CE1 A:CAS89 2.0 76.4 1.0 SG A:CAS89 2.2 66.2 1.0 CB A:CAS89 3.2 58.9 1.0 CA A:CAS89 3.8 51.7 1.0 OE2 A:GLU91 4.1 57.0 1.0 N A:ILE90 4.1 45.3 1.0 C A:CAS89 4.1 47.6 1.0 C A:ILE90 4.6 43.3 1.0 O A:ILE90 4.6 43.3 1.0 N A:GLU91 4.7 43.3 1.0 O A:CAS89 4.9 47.1 1.0 CD A:GLU91 5.0 53.6 1.0 CA A:ILE90 5.0 42.8 1.0

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


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:64.3 occ:1.00 AS C:CAS77 0.0 64.3 1.0 CE1 C:CAS77 2.0 63.0 1.0 CE2 C:CAS77 2.0 68.0 1.0 SG C:CAS77 2.2 55.7 1.0 CB C:CAS77 3.1 49.9 1.0 CA C:CAS77 3.6 45.4 1.0 CE K:MET45 4.2 67.0 1.0 C C:CAS77 4.3 42.4 1.0 CZ C:PHE148 4.3 63.1 1.0 O C:THR105 4.3 49.1 1.0 N C:ASN78 4.5 41.2 1.0 CA C:GLY106 4.5 51.3 1.0 C C:THR105 4.6 50.7 1.0 N C:GLY106 4.7 52.2 1.0 CE2 C:PHE148 4.8 60.7 1.0 N C:CAS77 4.8 42.2 1.0 O C:GLY104 4.9 53.7 1.0 NH2 C:ARG79 4.9 57.9 1.0 CG K:MET45 5.0 63.9 1.0 O C:PHE76 5.0 42.0 1.0 CZ C:ARG79 5.0 56.4 1.0

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


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:44.3 occ:1.00 AS D:CAS60 0.0 44.3 1.0 CE1 D:CAS60 2.0 45.2 1.0 CE2 D:CAS60 2.0 46.9 1.0 SG D:CAS60 2.2 42.2 1.0 CB D:CAS60 3.1 38.1 1.0 CA D:CAS60 3.4 36.0 1.0 N D:CAS60 4.0 35.7 1.0 CD2 D:LEU51 4.1 40.0 1.0 NE2 D:GLN49 4.3 40.7 1.0 C D:GLU59 4.5 36.2 1.0 O D:GLU59 4.5 36.1 1.0 C D:CAS60 4.7 34.6 1.0 CB D:LYS55 4.7 44.5 1.0 CG D:LYS55 4.7 45.9 1.0 CD D:GLN49 4.8 40.2 1.0 OE1 D:GLN49 4.9 39.0 1.0 O D:CAS60 5.0 34.4 1.0

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


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.5 occ:1.00 AS D:CAS89 0.0 0.5 1.0 CE1 D:CAS89 2.0 0.3 1.0 CE2 D:CAS89 2.0 0.9 1.0 SG D:CAS89 2.2 93.1 1.0 CB D:CAS89 3.1 85.0 1.0 CA D:CAS89 3.8 75.3 1.0 N D:ILE90 4.2 65.7 1.0 C D:CAS89 4.3 69.8 1.0 C D:ILE90 4.7 60.5 1.0 O D:ILE90 4.8 58.9 1.0 N D:GLU91 4.9 63.0 1.0

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


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:62.2 occ:1.00 AS F:CAS77 0.0 62.2 1.0 CE1 F:CAS77 2.0 61.1 1.0 CE2 F:CAS77 2.0 65.6 1.0 SG F:CAS77 2.2 52.2 1.0 CB F:CAS77 3.2 47.2 1.0 CA F:CAS77 3.7 43.8 1.0 CE H:MET45 4.2 77.1 1.0 CA F:GLY106 4.3 49.0 1.0 CZ F:PHE148 4.4 60.8 1.0 C F:CAS77 4.4 41.6 1.0 O F:THR105 4.4 44.1 1.0 N F:GLY106 4.5 48.9 1.0 C F:THR105 4.6 46.9 1.0 N F:ASN78 4.6 41.2 1.0 CE2 F:PHE148 4.7 58.7 1.0 CG H:MET45 4.8 76.1 1.0 N F:CAS77 5.0 41.2 1.0

Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6)


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:55.9 occ:1.00 AS G:CAS60 0.0 55.9 1.0 CE2 G:CAS60 2.0 57.3 1.0 CE1 G:CAS60 2.0 58.3 1.0 SG G:CAS60 2.2 52.5 1.0 CB G:CAS60 3.1 48.9 1.0 CA G:CAS60 3.3 47.5 1.0 NE2 G:GLN49 3.9 45.0 1.0 N G:CAS60 4.0 47.8 1.0 CD2 G:LEU51 4.0 50.2 1.0 C G:GLU59 4.6 49.0 1.0 C G:CAS60 4.6 45.3 1.0 CB G:LYS55 4.6 52.9 1.0 CG G:LYS55 4.7 54.5 1.0 CD G:GLN49 4.7 44.7 1.0 O G:GLU59 4.7 48.9 1.0 O G:CAS60 4.9 44.2 1.0 OE1 G:GLN49 5.0 44.0 1.0

Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6)


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:91.7 occ:1.00 AS G:CAS89 0.0 91.7 1.0 CE1 G:CAS89 2.0 86.5 1.0 CE2 G:CAS89 2.0 94.0 1.0 SG G:CAS89 2.2 73.1 1.0 CB G:CAS89 3.0 62.8 1.0 CA G:CAS89 3.7 55.3 1.0 C G:CAS89 4.3 50.6 1.0 N G:ILE90 4.3 45.8 1.0 O G:HOH212 4.7 42.0 1.0

Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6)


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:48.9 occ:1.00 AS I:CAS77 0.0 48.9 1.0 CE1 I:CAS77 2.0 48.7 1.0 CE2 I:CAS77 2.0 51.4 1.0 SG I:CAS77 2.2 43.4 1.0 CB I:CAS77 3.1 39.2 1.0 CA I:CAS77 3.6 36.1 1.0 CA I:GLY106 4.0 37.7 1.0 C I:CAS77 4.2 35.0 1.0 O I:THR105 4.2 34.4 1.0 N I:GLY106 4.3 36.6 1.0 C I:THR105 4.4 35.2 1.0 N I:ASN78 4.4 35.4 1.0 CE2 I:PHE148 4.7 44.3 1.0 N I:CAS77 4.8 34.9 1.0

Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6)


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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(3-Methyl-4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 6) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:53.0 occ:1.00 AS J:CAS60 0.0 53.0 1.0 CE2 J:CAS60 2.0 53.4 1.0 CE1 J:CAS60 2.0 53.8 1.0 SG J:CAS60 2.2 45.4 1.0 CB J:CAS60 3.2 39.3 1.0 CA J:CAS60 3.4 37.3 1.0 CD2 J:LEU51 4.0 34.5 1.0 N J:CAS60 4.0 36.4 1.0 NE2 J:GLN49 4.2 36.6 1.0 O J:GLU59 4.5 38.0 1.0 C J:GLU59 4.5 37.5 1.0 C J:CAS60 4.7 35.8 1.0 CB J:LYS55 4.7 36.7 1.0 CG J:LYS55 4.8 38.8 1.0 CD J:GLN49 4.8 35.2 1.0 O J:CAS60 4.9 35.2 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