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

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3), PDB code: 5nvv was solved by M.S.Gadd, P.Soares, C.Galdeano, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 2.10
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.299, 93.299, 364.958, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.5

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

Arsenic binding site 1 out of 12 in 5nvv

Go back to Arsenic Binding Sites List in 5nvv
Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:47.3
occ:1.00
 AS A:CAS60 0.0 47.3 1.0
CE2 A:CAS60 2.0 51.7 1.0
CE1 A:CAS60 2.0 49.9 1.0
SG A:CAS60 2.3 34.8 1.0
CB A:CAS60 3.2 29.1 1.0
CA A:CAS60 3.5 27.4 1.0
CD2 A:LEU51 3.7 29.7 1.0
N A:CAS60 4.2 25.9 1.0
O A:GLU59 4.5 26.9 1.0
CG A:LYS55 4.6 29.2 1.0
CB A:LYS55 4.6 26.6 1.0
NE2 A:GLN49 4.6 36.7 1.0
C A:GLU59 4.7 26.2 1.0
C A:CAS60 4.7 26.4 1.0
CD A:GLN49 4.8 35.6 1.0
O A:CAS60 4.9 26.5 1.0
CA A:LEU51 5.0 31.5 1.0

Arsenic binding site 2 out of 12 in 5nvv

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Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:55.6
occ:1.00
 AS A:CAS89 0.0 55.6 1.0
CE1 A:CAS89 2.0 60.1 1.0
CE2 A:CAS89 2.0 55.4 1.0
SG A:CAS89 2.2 45.7 1.0
CB A:CAS89 2.9 41.3 1.0
CA A:CAS89 3.4 38.0 1.0
C A:CAS89 4.0 34.1 1.0
N A:ILE90 4.1 34.5 1.0
OE2 A:GLU91 4.4 55.1 1.0
O A:ILE90 4.7 33.8 1.0
O A:HOH298 4.8 49.2 1.0
N A:CAS89 4.8 37.4 1.0
C A:ILE90 4.8 34.2 1.0
O A:LEU88 4.9 39.8 1.0
O A:CAS89 4.9 32.6 1.0

Arsenic binding site 3 out of 12 in 5nvv

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Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:44.4
occ:1.00
 AS C:CAS77 0.0 44.4 1.0
CE2 C:CAS77 2.0 46.7 1.0
CE1 C:CAS77 2.0 42.8 1.0
SG C:CAS77 2.2 34.2 1.0
CB C:CAS77 3.1 30.8 1.0
CA C:CAS77 3.5 27.6 1.0
CA C:GLY106 4.0 32.9 1.0
O C:THR105 4.2 29.8 1.0
C C:CAS77 4.3 27.2 1.0
N C:GLY106 4.3 32.0 1.0
C C:THR105 4.4 32.7 1.0
N C:ASN78 4.5 25.9 1.0
CZ K:PHE109 4.5 33.6 1.0
CE K:MET45 4.5 73.6 1.0
CE2 C:PHE148 4.6 46.5 1.0
CZ C:PHE148 4.6 47.5 1.0
N C:CAS77 4.7 25.6 1.0
NH2 C:ARG79 4.8 56.4 1.0
O C:PHE76 4.8 26.1 1.0
CG2 C:ILE75 5.0 29.3 1.0
SD K:MET45 5.0 77.8 1.0

Arsenic binding site 4 out of 12 in 5nvv

Go back to Arsenic Binding Sites List in 5nvv
Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:49.6
occ:1.00
 AS D:CAS60 0.0 49.6 1.0
CE1 D:CAS60 2.0 51.6 1.0
CE2 D:CAS60 2.0 54.8 1.0
SG D:CAS60 2.2 42.1 1.0
CB D:CAS60 3.1 35.5 1.0
CA D:CAS60 3.3 31.8 1.0
N D:CAS60 3.9 30.1 1.0
CD2 D:LEU51 4.3 39.6 1.0
O D:GLU59 4.3 29.5 1.0
C D:GLU59 4.4 30.0 1.0
NE2 D:GLN49 4.4 37.3 1.0
C D:CAS60 4.6 30.4 1.0
CB D:LYS55 4.6 39.2 1.0
CG D:LYS55 4.6 41.2 1.0
O D:CAS60 4.8 29.5 1.0
CD D:GLN49 4.9 36.8 1.0

Arsenic binding site 5 out of 12 in 5nvv

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Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:86.5
occ:1.00
 AS D:CAS89 0.0 86.5 1.0
CE1 D:CAS89 2.0 90.9 1.0
CE2 D:CAS89 2.0 84.4 1.0
SG D:CAS89 2.2 78.4 1.0
CB D:CAS89 2.9 71.4 1.0
CA D:CAS89 3.4 64.6 1.0
O D:HOH220 3.4 51.0 1.0
C D:CAS89 4.0 59.0 1.0
N D:ILE90 4.0 57.0 1.0
O D:HOH233 4.4 44.0 1.0
N D:CAS89 4.7 62.6 1.0
OE2 D:GLU91 4.7 80.0 1.0
O D:LEU88 4.8 63.3 1.0
O D:CAS89 4.9 56.2 1.0
C D:ILE90 4.9 54.7 1.0
O D:ILE90 5.0 56.2 1.0

Arsenic binding site 6 out of 12 in 5nvv

Go back to Arsenic Binding Sites List in 5nvv
Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:46.8
occ:1.00
 AS F:CAS77 0.0 46.8 1.0
CE1 F:CAS77 2.0 47.8 1.0
CE2 F:CAS77 2.0 48.8 1.0
SG F:CAS77 2.2 36.2 1.0
CB F:CAS77 3.1 31.8 1.0
CA F:CAS77 3.6 28.7 1.0
CA F:GLY106 4.0 37.8 1.0
O F:THR105 4.1 35.4 1.0
N F:GLY106 4.2 36.0 1.0
C F:THR105 4.3 37.4 1.0
CE H:MET45 4.3 61.9 1.0
C F:CAS77 4.3 28.1 1.0
CZ F:PHE148 4.4 53.9 1.0
N F:ASN78 4.6 26.7 1.0
CE2 F:PHE148 4.7 52.7 1.0
N F:CAS77 4.8 27.7 1.0
CG H:MET45 4.9 60.7 1.0
O F:PHE76 4.9 28.2 1.0

Arsenic binding site 7 out of 12 in 5nvv

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Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:51.8
occ:1.00
 AS G:CAS60 0.0 51.8 1.0
CE1 G:CAS60 2.0 52.3 1.0
CE2 G:CAS60 2.0 52.2 1.0
SG G:CAS60 2.2 44.8 1.0
CB G:CAS60 3.1 40.7 1.0
CA G:CAS60 3.4 40.7 1.0
CD2 G:LEU51 4.0 37.5 1.0
N G:CAS60 4.0 39.4 1.0
NE2 G:GLN49 4.1 38.8 1.0
C G:CAS60 4.6 39.1 1.0
C G:GLU59 4.6 42.2 1.0
O G:GLU59 4.6 43.2 1.0
CB G:LYS55 4.6 44.6 1.0
CD G:GLN49 4.7 36.2 1.0
CG G:LYS55 4.7 45.4 1.0
O G:CAS60 4.8 39.7 1.0

Arsenic binding site 8 out of 12 in 5nvv

Go back to Arsenic Binding Sites List in 5nvv
Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:61.8
occ:1.00
 AS G:CAS89 0.0 61.8 1.0
CE2 G:CAS89 2.0 59.8 1.0
CE1 G:CAS89 2.0 63.7 1.0
SG G:CAS89 2.2 44.7 1.0
CB G:CAS89 2.9 38.2 1.0
CA G:CAS89 3.5 35.4 1.0
C G:CAS89 4.0 31.6 1.0
N G:ILE90 4.1 30.7 1.0
O G:HOH212 4.4 34.8 1.0
O G:ILE90 4.6 29.7 1.0
C G:ILE90 4.8 29.8 1.0
N G:CAS89 4.8 35.4 1.0
O G:CAS89 4.9 29.8 1.0

Arsenic binding site 9 out of 12 in 5nvv

Go back to Arsenic Binding Sites List in 5nvv
Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As77

b:38.0
occ:1.00
 AS I:CAS77 0.0 38.0 1.0
CE2 I:CAS77 2.0 37.0 1.0
CE1 I:CAS77 2.0 40.0 1.0
SG I:CAS77 2.2 30.0 1.0
CB I:CAS77 3.1 26.0 1.0
CA I:CAS77 3.5 23.8 1.0
CA I:GLY106 3.8 27.1 1.0
N I:GLY106 3.9 27.6 1.0
O I:THR105 4.0 27.6 1.0
C I:THR105 4.1 28.5 1.0
C I:CAS77 4.1 23.5 1.0
N I:ASN78 4.2 23.8 1.0
N I:CAS77 4.8 22.0 1.0
O I:GLY104 4.8 33.7 1.0
O I:CAS77 4.9 24.6 1.0
O I:PHE76 5.0 21.7 1.0
CA I:THR105 5.0 30.0 1.0

Arsenic binding site 10 out of 12 in 5nvv

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Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-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)-4-Hydroxy-1-((S)-2-(2- Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As60

b:51.1
occ:1.00
 AS J:CAS60 0.0 51.1 1.0
CE1 J:CAS60 2.0 54.2 1.0
CE2 J:CAS60 2.0 55.8 1.0
SG J:CAS60 2.3 37.4 1.0
CB J:CAS60 3.2 31.0 1.0
CA J:CAS60 3.4 29.4 1.0
CD2 J:LEU51 4.0 28.5 1.0
N J:CAS60 4.1 28.0 1.0
NE2 J:GLN49 4.2 33.5 1.0
O J:GLU59 4.4 29.7 1.0
C J:GLU59 4.6 30.0 1.0
CG J:LYS55 4.6 33.8 1.0
CB J:LYS55 4.6 30.6 1.0
C J:CAS60 4.7 28.2 1.0
CD J:GLN49 4.8 31.3 1.0
O J:CAS60 4.9 26.4 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: Wed Jul 10 12:55:34 2024

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