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Arsenic in PDB 5nvy: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11), PDB code: 5nvy was solved by P.Soares, M.S.Gadd, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.76 / 2.90
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.085, 93.085, 362.983, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 26.9

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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) (pdb code 5nvy). 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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11), PDB code: 5nvy:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 12 in 5nvy

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Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:92.1
occ:1.00
 AS A:CAS60 0.0 92.1 1.0
CE1 A:CAS60 2.0 84.8 1.0
CE2 A:CAS60 2.0 82.1 1.0
SG A:CAS60 2.3 66.8 1.0
CB A:CAS60 3.3 55.7 1.0
CA A:CAS60 3.4 52.9 1.0
CD2 A:LEU51 4.0 48.9 1.0
N A:CAS60 4.0 51.6 1.0
O A:GLU59 4.2 53.2 1.0
C A:GLU59 4.4 52.4 1.0
CB A:LYS55 4.7 49.0 1.0
NE2 A:GLN49 4.7 57.3 1.0
C A:CAS60 4.7 50.5 1.0
CG A:LYS55 4.8 52.0 1.0
CB A:LEU51 4.9 48.0 1.0
CA A:LEU51 5.0 49.9 1.0
CG A:LEU51 5.0 47.4 1.0

Arsenic binding site 2 out of 12 in 5nvy

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Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) 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
CE1 A:CAS89 2.0 0.3 1.0
CE2 A:CAS89 2.0 0.2 1.0
SG A:CAS89 2.2 91.5 1.0
CB A:CAS89 3.1 78.0 1.0
CA A:CAS89 3.6 68.8 1.0
O A:HOH244 4.0 56.0 1.0
OE2 A:GLU91 4.1 67.0 1.0
C A:CAS89 4.3 62.4 1.0
N A:ILE90 4.3 59.1 1.0
N A:CAS89 4.9 65.8 1.0
O A:ILE90 4.9 56.0 1.0
O A:LEU88 5.0 66.0 1.0

Arsenic binding site 3 out of 12 in 5nvy

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Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:71.2
occ:1.00
 AS C:CAS77 0.0 71.2 1.0
CE2 C:CAS77 2.0 74.5 1.0
CE1 C:CAS77 2.0 69.7 1.0
SG C:CAS77 2.2 62.2 1.0
CB C:CAS77 3.1 56.6 1.0
CA C:CAS77 3.6 52.5 1.0
O C:THR105 4.3 53.5 1.0
C C:CAS77 4.3 50.5 1.0
CA C:GLY106 4.4 55.6 1.0
CZ K:PHE109 4.5 70.6 1.0
N C:ASN78 4.5 49.5 1.0
C C:THR105 4.5 55.3 1.0
CZ C:PHE148 4.5 77.6 1.0
CE K:MET45 4.6 88.9 1.0
N C:GLY106 4.6 56.5 1.0
N C:CAS77 4.9 49.7 1.0
SD K:MET45 4.9 90.9 1.0

Arsenic binding site 4 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:82.7
occ:1.00
 AS D:CAS60 0.0 82.7 1.0
CE1 D:CAS60 2.0 80.8 1.0
CE2 D:CAS60 2.0 81.1 1.0
SG D:CAS60 2.3 67.6 1.0
CB D:CAS60 3.2 60.3 1.0
CA D:CAS60 3.5 57.5 1.0
N D:CAS60 4.1 57.1 1.0
CD2 D:LEU51 4.1 58.4 1.0
O D:HOH211 4.2 56.7 1.0
O D:GLU59 4.5 59.1 1.0
NE2 D:GLN49 4.6 60.2 1.0
C D:GLU59 4.6 58.1 1.0
CB D:LYS55 4.6 65.7 1.0
CG D:LYS55 4.6 68.7 1.0
C D:CAS60 4.8 54.4 1.0
CD D:GLN49 4.9 59.0 1.0

Arsenic binding site 5 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:0.8
occ:1.00
 AS D:CAS89 0.0 0.8 1.0
CE1 D:CAS89 2.0 0.4 1.0
CE2 D:CAS89 2.0 0.2 1.0
SG D:CAS89 2.2 1.0 1.0
CB D:CAS89 3.1 0.3 1.0
CA D:CAS89 3.7 99.6 1.0
C D:CAS89 4.2 93.6 1.0
N D:ILE90 4.2 87.4 1.0
OE2 D:GLU91 4.3 0.3 1.0
O D:ILE90 4.7 78.2 1.0
C D:ILE90 4.8 79.0 1.0
O D:CAS89 5.0 95.6 1.0
N D:CAS89 5.0 93.7 1.0

Arsenic binding site 6 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:81.9
occ:1.00
 AS F:CAS77 0.0 81.9 1.0
CE2 F:CAS77 2.0 85.0 1.0
CE1 F:CAS77 2.0 80.9 1.0
SG F:CAS77 2.2 75.9 1.0
CB F:CAS77 3.3 66.0 1.0
CA F:CAS77 3.8 60.7 1.0
CA F:GLY106 4.3 58.1 1.0
CE H:MET45 4.3 98.2 1.0
N F:GLY106 4.4 59.0 1.0
O F:THR105 4.4 55.7 1.0
C F:CAS77 4.4 57.2 1.0
C F:THR105 4.4 58.1 1.0
CZ F:PHE148 4.6 68.9 1.0
N F:ASN78 4.7 55.4 1.0
NH2 F:ARG79 4.8 72.5 1.0
SD H:MET45 4.9 99.0 1.0
CZ H:PHE109 4.9 96.2 1.0
CE2 F:PHE148 4.9 67.4 1.0
CZ F:ARG79 4.9 70.5 1.0

Arsenic binding site 7 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:86.8
occ:1.00
 AS G:CAS60 0.0 86.8 1.0
CE2 G:CAS60 2.0 84.0 1.0
CE1 G:CAS60 2.0 86.0 1.0
SG G:CAS60 2.3 73.5 1.0
CB G:CAS60 3.2 66.5 1.0
CA G:CAS60 3.5 64.9 1.0
NE2 G:GLN49 4.0 65.0 1.0
N G:CAS60 4.1 64.8 1.0
CD2 G:LEU51 4.3 66.4 1.0
CG G:LYS55 4.5 74.2 1.0
CB G:LYS55 4.5 71.7 1.0
C G:GLU59 4.6 65.8 1.0
O G:GLU59 4.6 66.3 1.0
CD G:GLN49 4.6 64.5 1.0
C G:CAS60 4.9 63.2 1.0
OE1 G:GLN49 5.0 63.9 1.0

Arsenic binding site 8 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:0.9
occ:1.00
 AS G:CAS89 0.0 0.9 1.0
CE2 G:CAS89 2.0 0.7 1.0
CE1 G:CAS89 2.0 0.5 1.0
SG G:CAS89 2.2 92.6 1.0
CB G:CAS89 3.2 82.1 1.0
CA G:CAS89 3.8 73.7 1.0
N G:ILE90 4.1 63.6 1.0
C G:CAS89 4.3 67.5 1.0
C G:ILE90 4.7 59.7 1.0
O G:ILE90 4.7 60.7 1.0
N G:GLU91 4.8 58.6 1.0

Arsenic binding site 9 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As77

b:65.7
occ:1.00
 AS I:CAS77 0.0 65.7 1.0
CE2 I:CAS77 2.0 67.0 1.0
CE1 I:CAS77 2.0 67.5 1.0
SG I:CAS77 2.2 59.0 1.0
CB I:CAS77 3.2 51.5 1.0
CA I:CAS77 3.6 47.7 1.0
O I:THR105 3.7 44.4 1.0
CA I:GLY106 4.0 45.6 1.0
C I:THR105 4.0 45.5 1.0
N I:GLY106 4.1 46.3 1.0
C I:CAS77 4.2 46.5 1.0
N I:ASN78 4.2 46.6 1.0
N I:CAS77 4.9 45.7 1.0
CA I:THR105 5.0 46.8 1.0

Arsenic binding site 10 out of 12 in 5nvy

Go back to Arsenic Binding Sites List in 5nvy
Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11)


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-((S)-2-Acetamidopropanoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide (Ligand 11) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As60

b:93.2
occ:1.00
 AS J:CAS60 0.0 93.2 1.0
CE1 J:CAS60 2.0 89.9 1.0
CE2 J:CAS60 2.0 86.3 1.0
SG J:CAS60 2.3 74.7 1.0
CB J:CAS60 3.3 59.6 1.0
CA J:CAS60 3.5 56.1 1.0
CD2 J:LEU51 4.1 49.7 1.0
N J:CAS60 4.1 54.2 1.0
NE2 J:GLN49 4.4 54.7 1.0
O J:GLU59 4.4 55.1 1.0
C J:GLU59 4.5 54.7 1.0
CB J:LYS55 4.7 56.0 1.0
C J:CAS60 4.8 53.1 1.0
CG J:LYS55 4.8 59.0 1.0
CD J:GLN49 4.9 53.8 1.0

Reference:

P.Soares, M.S.Gadd, J.Frost, C.Galdeano, L.Ellis, O.Epemolu, S.Rocha, K.D.Read, A.Ciulli. Group-Based Optimization of Potent and Cell-Active Inhibitors of the Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3, 3-Dimethylbutanoyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (VH298). J. Med. Chem. V. 61 599 2018.
ISSN: ISSN 1520-4804
PubMed: 28853884
DOI: 10.1021/ACS.JMEDCHEM.7B00675
Page generated: Mon Jul 7 00:21:37 2025

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