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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)

Protein crystallography data

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

Arsenic Binding Sites:

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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

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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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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 4w9d

Go back to Arsenic Binding Sites List in 4w9d
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

Reference:

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
Page generated: Mon Jul 7 00:00:15 2025

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