Arsenic in PDB 4w9e: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4), PDB code: 4w9e 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 / 2.60
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.097, 93.097, 364.436, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 26.1

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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) (pdb code 4w9e). 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4), PDB code: 4w9e:
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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:77.8 occ:1.00 AS A:CAS60 0.0 77.8 1.0 CE2 A:CAS60 2.0 71.6 1.0 CE1 A:CAS60 2.0 76.9 1.0 SG A:CAS60 2.3 60.0 1.0 CB A:CAS60 3.2 48.1 1.0 CA A:CAS60 3.4 44.8 1.0 CD2 A:LEU51 3.8 39.4 1.0 N A:CAS60 4.0 43.7 1.0 CB A:LYS55 4.5 43.2 1.0 C A:GLU59 4.5 45.7 1.0 NE2 A:GLN49 4.5 48.9 1.0 O A:GLU59 4.6 44.8 1.0 CG A:LYS55 4.6 46.5 1.0 C A:CAS60 4.7 42.1 1.0 CD A:GLN49 4.9 47.3 1.0 O A:CAS60 5.0 41.7 1.0 OE1 A:GLN49 5.0 48.0 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:95.3 occ:1.00 AS A:CAS89 0.0 95.3 1.0 CE2 A:CAS89 2.0 95.3 1.0 CE1 A:CAS89 2.0 92.2 1.0 SG A:CAS89 2.2 80.7 1.0 CB A:CAS89 3.2 67.6 1.0 CA A:CAS89 3.6 58.0 1.0 N A:ILE90 3.9 52.5 1.0 C A:CAS89 4.0 53.4 1.0 OE2 A:GLU91 4.3 77.4 1.0 C A:ILE90 4.5 50.5 1.0 O A:ILE90 4.5 50.0 1.0 N A:GLU91 4.8 50.4 1.0 CA A:ILE90 4.8 50.2 1.0 O A:CAS89 5.0 51.5 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:70.8 occ:1.00 AS C:CAS77 0.0 70.8 1.0 CE1 C:CAS77 2.0 69.4 1.0 CE2 C:CAS77 2.0 72.5 1.0 SG C:CAS77 2.2 60.8 1.0 CB C:CAS77 3.1 54.6 1.0 CA C:CAS77 3.6 48.3 1.0 CE K:MET45 4.2 86.7 1.0 CA C:GLY106 4.3 49.8 1.0 O C:THR105 4.3 45.6 1.0 CZ C:PHE148 4.3 72.0 1.0 C C:CAS77 4.4 46.1 1.0 N C:GLY106 4.5 50.1 1.0 C C:THR105 4.5 49.1 1.0 N C:ASN78 4.6 44.2 1.0 CZ K:PHE109 4.8 67.8 1.0 N C:CAS77 4.9 45.1 1.0 O C:PHE76 4.9 46.7 1.0 SD K:MET45 5.0 87.1 1.0 CE2 C:PHE148 5.0 71.0 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:65.2 occ:1.00 AS D:CAS60 0.0 65.2 1.0 CE1 D:CAS60 2.0 65.6 1.0 CE2 D:CAS60 2.0 68.6 1.0 SG D:CAS60 2.2 57.5 1.0 CB D:CAS60 3.2 48.5 1.0 CA D:CAS60 3.4 44.1 1.0 CD2 D:LEU51 4.0 48.1 1.0 N D:CAS60 4.1 43.0 1.0 O D:GLU59 4.4 44.3 1.0 C D:GLU59 4.5 44.4 1.0 CB D:LYS55 4.6 57.0 1.0 NE2 D:GLN49 4.6 47.5 1.0 CG D:LYS55 4.6 57.8 1.0 C D:CAS60 4.7 42.8 1.0 CD D:GLN49 4.9 46.9 1.0 O D:CAS60 4.9 42.4 1.0 OE1 D:GLN49 4.9 46.1 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.4 occ:1.00 AS D:CAS89 0.0 0.4 1.0 CE2 D:CAS89 2.0 0.2 1.0 CE1 D:CAS89 2.0 0.4 1.0 SG D:CAS89 2.2 0.6 1.0 CB D:CAS89 3.2 90.3 1.0 CA D:CAS89 3.7 80.3 1.0 N D:ILE90 4.1 70.8 1.0 C D:CAS89 4.2 75.8 1.0 O D:ILE90 4.6 59.4 1.0 C D:ILE90 4.7 62.9 1.0 N D:GLU91 5.0 67.4 1.0 N D:CAS89 5.0 75.0 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:67.0 occ:1.00 AS F:CAS77 0.0 67.0 1.0 CE1 F:CAS77 2.0 67.3 1.0 CE2 F:CAS77 2.0 69.2 1.0 SG F:CAS77 2.2 56.7 1.0 CB F:CAS77 3.2 50.3 1.0 CA F:CAS77 3.7 47.0 1.0 CE H:MET45 4.1 83.3 1.0 CA F:GLY106 4.2 54.1 1.0 CZ F:PHE148 4.2 63.9 1.0 O F:THR105 4.3 43.1 1.0 N F:GLY106 4.4 53.8 1.0 C F:THR105 4.5 50.5 1.0 C F:CAS77 4.5 44.5 1.0 N F:ASN78 4.7 43.3 1.0 CG H:MET45 4.7 82.3 1.0 SD H:MET45 4.8 84.8 1.0 CE2 F:PHE148 4.9 63.9 1.0 N F:CAS77 5.0 45.5 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:69.9 occ:1.00 AS G:CAS60 0.0 69.9 1.0 CE1 G:CAS60 2.0 72.5 1.0 CE2 G:CAS60 2.0 70.0 1.0 SG G:CAS60 2.2 60.6 1.0 CB G:CAS60 3.2 55.6 1.0 CA G:CAS60 3.4 52.6 1.0 CD2 G:LEU51 4.0 55.1 1.0 N G:CAS60 4.0 52.1 1.0 NE2 G:GLN49 4.4 48.8 1.0 CB G:LYS55 4.6 66.3 1.0 C G:GLU59 4.6 56.5 1.0 CG G:LYS55 4.6 69.8 1.0 C G:CAS60 4.6 53.6 1.0 O G:GLU59 4.7 56.2 1.0 CD G:GLN49 4.8 48.5 1.0 O G:CAS60 4.9 54.3 1.0 OE1 G:GLN49 5.0 49.1 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:99.5 occ:1.00 AS G:CAS89 0.0 99.5 1.0 CE1 G:CAS89 2.0 93.2 1.0 CE2 G:CAS89 2.0 0.4 1.0 SG G:CAS89 2.2 72.4 1.0 CB G:CAS89 3.1 60.9 1.0 CA G:CAS89 3.8 52.6 1.0 C G:CAS89 4.3 49.1 1.0 N G:ILE90 4.3 46.5 1.0 O G:HOH213 4.8 58.1 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:60.0 occ:1.00 AS I:CAS77 0.0 60.0 1.0 CE2 I:CAS77 2.0 63.1 1.0 CE1 I:CAS77 2.0 63.0 1.0 SG I:CAS77 2.2 55.0 1.0 CB I:CAS77 3.1 45.6 1.0 CA I:CAS77 3.6 40.1 1.0 O I:THR105 4.0 41.8 1.0 CA I:GLY106 4.0 42.3 1.0 C I:THR105 4.2 42.2 1.0 N I:GLY106 4.3 41.7 1.0 C I:CAS77 4.3 38.5 1.0 N I:ASN78 4.4 38.3 1.0 N I:CAS77 4.8 39.8 1.0 CZ I:PHE148 4.9 58.7 1.0 CE2 I:PHE148 4.9 59.1 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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)


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-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:75.5 occ:1.00 AS J:CAS60 0.0 75.5 1.0 CE2 J:CAS60 2.0 73.6 1.0 CE1 J:CAS60 2.0 73.5 1.0 SG J:CAS60 2.3 59.2 1.0 CB J:CAS60 3.3 47.9 1.0 CA J:CAS60 3.4 43.9 1.0 CD2 J:LEU51 4.0 43.6 1.0 N J:CAS60 4.1 42.0 1.0 NE2 J:GLN49 4.4 44.7 1.0 O J:GLU59 4.5 47.4 1.0 C J:GLU59 4.6 45.0 1.0 CB J:LYS55 4.6 45.5 1.0 CG J:LYS55 4.6 48.5 1.0 C J:CAS60 4.7 41.5 1.0 CD J:GLN49 4.9 42.7 1.0 O J:CAS60 4.9 39.5 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