Arsenic in PDB 4w9c: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2), PDB code: 4w9c was solved by M.S.Gadd, S.Hewitt, 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)	93.78 / 2.20
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.779, 93.779, 366.034, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.1

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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) (pdb code 4w9c). 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2), PDB code: 4w9c:
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:55.7 occ:1.00 AS A:CAS60 0.0 55.7 1.0 CE2 A:CAS60 2.0 55.9 1.0 CE1 A:CAS60 2.0 56.8 1.0 SG A:CAS60 2.3 38.4 1.0 CB A:CAS60 3.2 31.2 1.0 CA A:CAS60 3.4 28.5 1.0 CD2 A:LEU51 3.8 31.5 1.0 N A:CAS60 4.0 27.7 1.0 O A:GLU59 4.4 27.6 1.0 NE2 A:GLN49 4.5 37.6 1.0 C A:GLU59 4.5 27.5 1.0 CB A:LYS55 4.5 27.9 1.0 CG A:LYS55 4.6 30.4 1.0 C A:CAS60 4.7 28.8 1.0 O A:CAS60 5.0 29.9 1.0 CD A:GLN49 5.0 36.4 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:67.5 occ:1.00 AS A:CAS89 0.0 67.5 1.0 CE1 A:CAS89 2.0 69.2 1.0 CE2 A:CAS89 2.0 69.7 1.0 SG A:CAS89 2.2 53.6 1.0 CB A:CAS89 3.1 47.9 1.0 CA A:CAS89 3.7 42.8 1.0 N A:ILE90 4.1 38.0 1.0 C A:CAS89 4.2 38.3 1.0 O A:HOH256 4.4 40.8 1.0 OE2 A:GLU91 4.6 61.3 1.0 O A:ILE90 4.7 36.2 1.0 C A:ILE90 4.8 36.9 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:55.3 occ:1.00 AS C:CAS77 0.0 55.3 1.0 CE1 C:CAS77 2.0 56.5 1.0 CE2 C:CAS77 2.0 58.5 1.0 SG C:CAS77 2.2 43.3 1.0 CB C:CAS77 3.1 37.4 1.0 CA C:CAS77 3.6 33.2 1.0 CE K:MET45 3.8 68.4 1.0 CA C:GLY106 4.3 39.7 1.0 O C:THR105 4.4 40.6 1.0 C C:CAS77 4.4 33.0 1.0 CZ C:PHE148 4.5 63.4 1.0 N C:GLY106 4.6 39.8 1.0 C C:THR105 4.6 40.6 1.0 N C:ASN78 4.6 32.0 1.0 CG K:MET45 4.8 61.8 1.0 CE2 C:PHE148 4.9 63.6 1.0 N C:CAS77 4.9 31.5 1.0 SD K:MET45 4.9 66.8 1.0 O C:PHE76 5.0 30.9 1.0 NH2 C:ARG79 5.0 69.3 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:47.1 occ:1.00 AS D:CAS60 0.0 47.1 1.0 CE1 D:CAS60 2.0 49.6 1.0 CE2 D:CAS60 2.0 52.6 1.0 SG D:CAS60 2.2 40.8 1.0 CB D:CAS60 3.2 34.0 1.0 CA D:CAS60 3.4 31.4 1.0 N D:CAS60 4.0 30.6 1.0 CD2 D:LEU51 4.3 42.8 1.0 NE2 D:GLN49 4.3 37.3 1.0 O D:GLU59 4.4 30.9 1.0 C D:GLU59 4.4 30.8 1.0 C D:CAS60 4.6 29.0 1.0 CG D:LYS55 4.7 41.7 1.0 CB D:LYS55 4.8 40.4 1.0 CD D:GLN49 4.9 36.7 1.0 O D:CAS60 4.9 28.9 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) 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 0.0 1.0 CE2 D:CAS89 2.0 0.5 1.0 SG D:CAS89 2.2 94.0 1.0 CB D:CAS89 3.1 81.1 1.0 CA D:CAS89 3.7 72.4 1.0 N D:ILE90 4.3 62.1 1.0 C D:CAS89 4.3 66.0 1.0 O D:HOH224 4.7 61.2 1.0 OE1 D:GLU91 4.9 82.5 1.0 C D:ILE90 4.9 57.0 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:55.2 occ:1.00 AS F:CAS77 0.0 55.2 1.0 CE1 F:CAS77 2.0 54.1 1.0 CE2 F:CAS77 2.0 56.8 1.0 SG F:CAS77 2.2 45.0 1.0 CB F:CAS77 3.1 39.0 1.0 CA F:CAS77 3.7 35.1 1.0 CE H:MET45 4.1 75.3 1.0 CA F:GLY106 4.2 40.8 1.0 O F:THR105 4.3 35.5 1.0 N F:GLY106 4.4 39.5 1.0 C F:CAS77 4.4 33.2 1.0 C F:THR105 4.4 38.8 1.0 CZ F:PHE148 4.5 56.5 1.0 N F:ASN78 4.6 32.1 1.0 CG H:MET45 4.8 68.0 1.0 CE2 F:PHE148 4.8 54.9 1.0 SD H:MET45 4.9 74.7 1.0 N F:CAS77 4.9 33.7 1.0 O F:PHE76 5.0 32.9 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:51.5 occ:1.00 AS G:CAS60 0.0 51.5 1.0 CE2 G:CAS60 2.0 52.5 1.0 CE1 G:CAS60 2.0 52.5 1.0 SG G:CAS60 2.2 49.0 1.0 CB G:CAS60 3.1 42.9 1.0 CA G:CAS60 3.3 41.3 1.0 CD2 G:LEU51 3.9 37.5 1.0 N G:CAS60 4.0 40.3 1.0 NE2 G:GLN49 4.2 36.1 1.0 C G:CAS60 4.5 40.1 1.0 C G:GLU59 4.6 41.4 1.0 O G:GLU59 4.6 41.1 1.0 CD G:GLN49 4.6 34.9 1.0 CB G:LYS55 4.6 45.2 1.0 CG G:LYS55 4.6 47.6 1.0 O G:CAS60 4.8 40.4 1.0 OE1 G:GLN49 4.8 34.2 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:66.3 occ:1.00 AS G:CAS89 0.0 66.3 1.0 CE1 G:CAS89 2.0 64.7 1.0 CE2 G:CAS89 2.0 71.3 1.0 SG G:CAS89 2.2 51.1 1.0 CB G:CAS89 3.0 41.2 1.0 O G:HOH240 3.3 46.8 1.0 CA G:CAS89 3.5 36.9 1.0 O G:HOH236 3.8 44.2 1.0 O G:HOH224 3.8 43.1 1.0 N G:ILE90 4.0 33.2 1.0 C G:CAS89 4.1 33.3 1.0 O G:ILE90 4.6 32.5 1.0 C G:ILE90 4.8 32.8 1.0 N G:CAS89 4.9 37.0 1.0 O G:LEU88 5.0 40.9 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:44.3 occ:1.00 AS I:CAS77 0.0 44.3 1.0 CE1 I:CAS77 2.0 46.5 1.0 CE2 I:CAS77 2.0 44.9 1.0 SG I:CAS77 2.2 38.6 1.0 CB I:CAS77 3.1 32.4 1.0 CA I:CAS77 3.5 28.9 1.0 CA I:GLY106 3.9 33.1 1.0 O I:THR105 4.1 32.5 1.0 C I:CAS77 4.2 27.9 1.0 N I:GLY106 4.2 32.9 1.0 C I:THR105 4.3 33.4 1.0 N I:ASN78 4.3 27.5 1.0 N I:CAS77 4.8 26.9 1.0 CE2 I:PHE148 4.9 40.0 1.0 O I:PHE76 5.0 28.2 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)


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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:49.5 occ:1.00 AS J:CAS60 0.0 49.5 1.0 CE2 J:CAS60 2.0 53.7 1.0 CE1 J:CAS60 2.0 52.7 1.0 SG J:CAS60 2.3 40.9 1.0 CB J:CAS60 3.3 33.0 1.0 CA J:CAS60 3.5 30.5 1.0 CD2 J:LEU51 3.9 30.0 1.0 N J:CAS60 4.1 28.9 1.0 O J:GLU59 4.4 29.7 1.0 NE2 J:GLN49 4.5 35.3 1.0 C J:GLU59 4.6 30.0 1.0 CG J:LYS55 4.6 32.7 1.0 CB J:LYS55 4.7 30.4 1.0 C J:CAS60 4.7 29.8 1.0 CD J:GLN49 4.9 33.4 1.0 O J:CAS60 4.9 30.1 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