Arsenic in PDB 4w9d: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3), PDB code: 4w9d 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)	93.90 / 2.20
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.901, 93.901, 365.869, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.6

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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) (pdb code 4w9d). 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3), PDB code: 4w9d:
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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:As60 b:96.1 occ:1.00 AS A:CAS60 0.0 96.1 1.0 CE1 A:CAS60 2.0 98.2 1.0 CE2 A:CAS60 2.0 85.1 1.0 SG A:CAS60 2.3 56.9 1.0 CB A:CAS60 3.2 45.1 1.0 CA A:CAS60 3.4 40.4 1.0 CD2 A:LEU51 3.8 43.9 1.0 N A:CAS60 4.0 38.3 1.0 CG A:LYS55 4.4 44.6 1.0 CB A:LYS55 4.4 38.8 1.0 O A:GLU59 4.5 40.8 1.0 C A:GLU59 4.5 40.8 1.0 C A:CAS60 4.6 39.9 1.0 CD A:LYS55 4.9 48.3 1.0 CA A:LEU51 4.9 44.0 1.0 O A:CAS60 4.9 40.6 1.0 CB A:LEU51 4.9 42.9 1.0 CG A:LEU51 5.0 44.2 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-(4-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ A:As89 b:0.8 occ:1.00 AS A:CAS89 0.0 0.8 1.0 CE2 A:CAS89 2.0 0.7 1.0 CE1 A:CAS89 2.0 0.3 1.0 SG A:CAS89 2.2 91.3 1.0 CB A:CAS89 3.2 68.4 1.0 OE2 A:GLU91 3.6 88.9 1.0 CA A:CAS89 3.8 59.6 1.0 C A:CAS89 4.2 51.8 1.0 N A:ILE90 4.2 51.3 1.0 CD A:GLU91 4.5 79.6 1.0 O A:ILE90 4.6 47.8 1.0 C A:ILE90 4.7 48.3 1.0 N A:GLU91 4.9 47.7 1.0 O A:CAS89 4.9 47.3 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ C:As77 b:74.1 occ:1.00 AS C:CAS77 0.0 74.1 1.0 CE1 C:CAS77 2.0 75.3 1.0 CE2 C:CAS77 2.0 69.9 1.0 SG C:CAS77 2.2 50.1 1.0 CB C:CAS77 3.2 44.1 1.0 CA C:CAS77 3.7 38.7 1.0 CA C:GLY106 4.2 43.8 1.0 CE K:MET45 4.3 82.5 1.0 CE2 C:PHE148 4.4 65.2 1.0 O C:THR105 4.4 46.7 1.0 N C:GLY106 4.4 44.1 1.0 C C:CAS77 4.4 37.0 1.0 CZ C:PHE148 4.5 66.3 1.0 C C:THR105 4.5 46.1 1.0 CZ K:PHE109 4.6 48.4 1.0 N C:ASN78 4.6 35.0 1.0 NH2 C:ARG79 4.8 86.8 1.0 N C:CAS77 4.9 36.9 1.0 O C:PHE76 5.0 38.2 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ D:As60 b:84.4 occ:1.00 AS D:CAS60 0.0 84.4 1.0 CE1 D:CAS60 2.0 89.1 1.0 CE2 D:CAS60 2.0 82.5 1.0 SG D:CAS60 2.3 67.2 1.0 CB D:CAS60 3.2 50.5 1.0 CA D:CAS60 3.5 44.7 1.0 N D:CAS60 4.0 42.5 1.0 CD2 D:LEU51 4.1 55.9 1.0 O D:GLU59 4.4 43.6 1.0 C D:GLU59 4.5 41.3 1.0 CG D:LYS55 4.5 62.0 1.0 CB D:LYS55 4.6 58.8 1.0 NE2 D:GLN49 4.7 55.2 1.0 C D:CAS60 4.8 41.6 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ D:As89 b:0.0 occ:1.00 AS D:CAS89 0.0 0.0 1.0 CE1 D:CAS89 2.0 0.8 1.0 CE2 D:CAS89 2.0 0.2 1.0 SG D:CAS89 2.2 0.2 1.0 CB D:CAS89 3.2 99.3 1.0 CA D:CAS89 3.8 82.6 1.0 N D:ILE90 4.2 70.8 1.0 C D:CAS89 4.2 73.0 1.0 C D:ILE90 4.8 67.6 1.0 O D:ILE90 4.9 72.4 1.0 N D:GLU91 5.0 70.1 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ F:As77 b:77.4 occ:1.00 AS F:CAS77 0.0 77.4 1.0 CE1 F:CAS77 2.0 79.2 1.0 CE2 F:CAS77 2.0 78.3 1.0 SG F:CAS77 2.2 56.1 1.0 CB F:CAS77 3.2 46.0 1.0 CA F:CAS77 3.7 39.1 1.0 CA F:GLY106 4.2 47.0 1.0 CE H:MET45 4.2 87.5 1.0 N F:GLY106 4.4 44.6 1.0 O F:THR105 4.4 39.1 1.0 C F:CAS77 4.5 36.2 1.0 CZ F:PHE148 4.5 67.9 1.0 C F:THR105 4.5 45.4 1.0 CE2 F:PHE148 4.7 68.8 1.0 N F:ASN78 4.8 35.5 1.0 NH2 F:ARG79 4.9 86.2 1.0 N F:CAS77 4.9 40.6 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ G:As60 b:81.8 occ:1.00 AS G:CAS60 0.0 81.8 1.0 CE1 G:CAS60 2.0 83.0 1.0 CE2 G:CAS60 2.0 80.7 1.0 SG G:CAS60 2.3 64.0 1.0 CB G:CAS60 3.2 52.7 1.0 CA G:CAS60 3.5 48.5 1.0 CD2 G:LEU51 4.1 58.0 1.0 N G:CAS60 4.1 46.3 1.0 NE2 G:GLN49 4.3 51.0 1.0 CG G:LYS55 4.5 68.3 1.0 CB G:LYS55 4.6 62.9 1.0 C G:GLU59 4.7 52.0 1.0 C G:CAS60 4.7 49.5 1.0 O G:GLU59 4.7 51.4 1.0 CD G:GLN49 4.8 48.9 1.0 O G:CAS60 4.9 53.0 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-(4-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ G:As89 b:0.4 occ:1.00 AS G:CAS89 0.0 0.4 1.0 CE1 G:CAS89 2.0 0.8 1.0 CE2 G:CAS89 2.0 0.5 1.0 SG G:CAS89 2.2 98.0 1.0 CB G:CAS89 3.1 66.5 1.0 CA G:CAS89 3.8 55.4 1.0 N G:ILE90 4.3 48.8 1.0 C G:CAS89 4.3 50.3 1.0 O G:HOH212 4.4 58.9 1.0 O G:ILE90 4.9 45.4 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ I:As77 b:70.6 occ:1.00 AS I:CAS77 0.0 70.6 1.0 CE2 I:CAS77 2.0 68.5 1.0 CE1 I:CAS77 2.0 74.8 1.0 SG I:CAS77 2.2 53.0 1.0 CB I:CAS77 3.1 40.2 1.0 CA I:CAS77 3.5 35.0 1.0 CA I:GLY106 3.9 42.6 1.0 O I:THR105 4.1 39.1 1.0 N I:GLY106 4.2 39.6 1.0 C I:CAS77 4.2 32.8 1.0 C I:THR105 4.3 42.1 1.0 N I:ASN78 4.4 33.9 1.0 CE2 I:PHE148 4.8 59.8 1.0 N I:CAS77 4.8 34.5 1.0 O I:PHE76 4.9 40.2 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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)


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-(4-Methyloxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range: probe atom residue distance (Å) B Occ J:As60 b:87.8 occ:1.00 AS J:CAS60 0.0 87.8 1.0 CE2 J:CAS60 2.0 84.3 1.0 CE1 J:CAS60 2.0 91.0 1.0 SG J:CAS60 2.3 59.0 1.0 CB J:CAS60 3.3 47.6 1.0 CA J:CAS60 3.5 41.3 1.0 CD2 J:LEU51 3.9 46.1 1.0 N J:CAS60 4.2 38.7 1.0 O J:GLU59 4.4 40.4 1.0 CG J:LYS55 4.5 49.8 1.0 CB J:LYS55 4.5 46.1 1.0 C J:GLU59 4.6 42.0 1.0 C J:CAS60 4.7 41.5 1.0 NE2 J:GLN49 4.9 48.4 1.0 O J:CAS60 4.9 41.8 1.0 CA J:LEU51 4.9 40.7 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