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Arsenic in PDB 5nw0: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17), PDB code: 5nw0 was solved by M.S.Gadd, P.Soares, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.57 / 2.30
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 94.771, 94.771, 368.359, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 23.9

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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) (pdb code 5nw0). 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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17), PDB code: 5nw0:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 12 in 5nw0

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Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:50.9
occ:1.00
 AS A:CAS60 0.0 50.9 1.0
CE1 A:CAS60 2.0 55.3 1.0
CE2 A:CAS60 2.0 58.4 1.0
SG A:CAS60 2.3 37.8 1.0
CB A:CAS60 3.2 30.2 1.0
CA A:CAS60 3.5 28.8 1.0
CD2 A:LEU51 3.8 32.5 1.0
N A:CAS60 4.2 27.4 1.0
O A:GLU59 4.6 30.1 1.0
C A:CAS60 4.7 28.6 1.0
C A:GLU59 4.7 29.5 1.0
CG A:LYS55 4.7 34.2 1.0
CB A:LYS55 4.7 31.0 1.0
NE2 A:GLN49 4.8 39.4 1.0
O A:CAS60 4.9 28.5 1.0

Arsenic binding site 2 out of 12 in 5nw0

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Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:68.2
occ:1.00
 AS A:CAS89 0.0 68.2 1.0
CE1 A:CAS89 2.0 71.2 1.0
CE2 A:CAS89 2.0 67.0 1.0
SG A:CAS89 2.2 58.0 1.0
CB A:CAS89 3.0 52.5 1.0
CA A:CAS89 3.5 47.4 1.0
N A:ILE90 4.1 42.5 1.0
C A:CAS89 4.1 42.8 1.0
OE2 A:GLU91 4.6 66.6 1.0
O A:HOH297 4.7 53.8 1.0
N A:CAS89 4.8 47.4 1.0
O A:ILE90 4.8 43.0 1.0
C A:ILE90 4.9 41.7 1.0
O A:LEU88 4.9 50.2 1.0
O A:CAS89 5.0 40.3 1.0

Arsenic binding site 3 out of 12 in 5nw0

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Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:67.6
occ:1.00
 AS C:CAS77 0.0 67.6 1.0
CE1 C:CAS77 2.0 64.0 1.0
CE2 C:CAS77 2.0 66.2 1.0
SG C:CAS77 2.2 52.0 1.0
CB C:CAS77 3.1 44.7 1.0
CA C:CAS77 3.6 38.8 1.0
CA C:GLY106 4.1 40.2 1.0
C C:CAS77 4.4 37.3 1.0
N C:GLY106 4.4 39.1 1.0
CE K:MET45 4.5 91.8 1.0
O C:THR105 4.5 39.3 1.0
CE2 C:PHE148 4.6 66.8 1.0
C C:THR105 4.6 41.0 1.0
N C:ASN78 4.6 35.6 1.0
CZ C:PHE148 4.7 69.3 1.0
CZ K:PHE109 4.7 43.8 1.0
N C:CAS77 4.8 37.3 1.0
NH2 C:ARG79 4.9 56.9 1.0
O C:GLY104 4.9 49.8 1.0
O C:PHE76 4.9 35.7 1.0
SD K:MET45 4.9 90.0 1.0

Arsenic binding site 4 out of 12 in 5nw0

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Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:50.3
occ:1.00
 AS D:CAS60 0.0 50.3 1.0
CE2 D:CAS60 2.0 57.4 1.0
CE1 D:CAS60 2.0 53.3 1.0
SG D:CAS60 2.2 45.8 1.0
CB D:CAS60 3.1 39.0 1.0
CA D:CAS60 3.3 35.0 1.0
N D:CAS60 3.9 33.2 1.0
O D:GLU59 4.4 32.0 1.0
CD2 D:LEU51 4.4 44.1 1.0
C D:GLU59 4.4 33.0 1.0
NE2 D:GLN49 4.4 42.5 1.0
C D:CAS60 4.6 33.3 1.0
O D:CAS60 4.8 33.5 1.0
CG D:LYS55 4.8 49.7 1.0
CD D:GLN49 4.9 41.7 1.0
CB D:LYS55 4.9 47.1 1.0

Arsenic binding site 5 out of 12 in 5nw0

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Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:1.0
occ:1.00
 AS D:CAS89 0.0 1.0 1.0
CE1 D:CAS89 2.0 1.0 1.0
CE2 D:CAS89 2.0 0.1 1.0
SG D:CAS89 2.2 98.8 1.0
CB D:CAS89 3.0 89.8 1.0
O D:HOH219 3.5 57.9 1.0
CA D:CAS89 3.5 79.3 1.0
C D:CAS89 4.2 71.5 1.0
N D:ILE90 4.2 68.2 1.0
OE2 D:GLU91 4.5 90.8 1.0
O D:HOH206 4.7 70.8 1.0
N D:CAS89 4.8 76.8 1.0
O D:LEU88 4.9 78.9 1.0

Arsenic binding site 6 out of 12 in 5nw0

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Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:73.7
occ:1.00
 AS F:CAS77 0.0 73.7 1.0
CE1 F:CAS77 2.0 71.2 1.0
CE2 F:CAS77 2.0 75.2 1.0
SG F:CAS77 2.2 60.0 1.0
CB F:CAS77 3.1 53.1 1.0
CA F:CAS77 3.7 48.4 1.0
CA F:GLY106 4.2 52.2 1.0
CE H:MET45 4.3 98.6 1.0
O F:THR105 4.4 48.7 1.0
C F:CAS77 4.4 44.7 1.0
N F:GLY106 4.5 50.6 1.0
C F:THR105 4.5 51.8 1.0
N F:ASN78 4.7 41.9 1.0
CE2 F:PHE148 4.7 73.9 1.0
CZ F:PHE148 4.8 76.4 1.0
N F:CAS77 4.9 47.2 1.0

Arsenic binding site 7 out of 12 in 5nw0

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Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:60.0
occ:1.00
 AS G:CAS60 0.0 60.0 1.0
CE1 G:CAS60 2.0 56.7 1.0
CE2 G:CAS60 2.0 59.4 1.0
SG G:CAS60 2.2 54.2 1.0
CB G:CAS60 3.1 52.2 1.0
CA G:CAS60 3.4 49.6 1.0
CD2 G:LEU51 4.0 51.4 1.0
N G:CAS60 4.0 48.5 1.0
NE2 G:GLN49 4.3 46.7 1.0
C G:GLU59 4.6 50.9 1.0
C G:CAS60 4.6 50.1 1.0
O G:GLU59 4.7 51.8 1.0
CD G:GLN49 4.7 44.8 1.0
CB G:LYS55 4.8 55.3 1.0
O G:CAS60 4.8 49.7 1.0
OE1 G:GLN49 4.9 42.6 1.0
CG G:LYS55 4.9 56.8 1.0

Arsenic binding site 8 out of 12 in 5nw0

Go back to Arsenic Binding Sites List in 5nw0
Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:91.9
occ:1.00
 AS G:CAS89 0.0 91.9 1.0
CE2 G:CAS89 2.0 87.5 1.0
CE1 G:CAS89 2.0 95.7 1.0
SG G:CAS89 2.2 71.6 1.0
CB G:CAS89 3.1 58.2 1.0
CA G:CAS89 3.6 51.5 1.0
O G:HOH224 3.7 49.0 1.0
N G:ILE90 4.1 44.0 1.0
C G:CAS89 4.1 45.7 1.0
O G:HOH209 4.3 42.5 1.0
O G:ILE90 4.7 43.2 1.0
C G:ILE90 4.8 43.7 1.0
N G:CAS89 5.0 50.8 1.0

Arsenic binding site 9 out of 12 in 5nw0

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Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As77

b:53.6
occ:1.00
 AS I:CAS77 0.0 53.6 1.0
CE1 I:CAS77 2.0 58.4 1.0
CE2 I:CAS77 2.0 51.4 1.0
SG I:CAS77 2.2 41.3 1.0
CB I:CAS77 3.2 34.8 1.0
CA I:CAS77 3.5 31.1 1.0
CA I:GLY106 3.9 32.1 1.0
N I:GLY106 4.1 31.9 1.0
C I:CAS77 4.2 30.0 1.0
O I:THR105 4.2 31.0 1.0
C I:THR105 4.2 33.5 1.0
N I:ASN78 4.3 29.7 1.0
N I:CAS77 4.8 29.4 1.0

Arsenic binding site 10 out of 12 in 5nw0

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Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17)


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-(1- Acetamidocyclopropanecarboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N- (4-(4-Methylthiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As60

b:51.8
occ:1.00
 AS J:CAS60 0.0 51.8 1.0
CE2 J:CAS60 2.0 55.1 1.0
CE1 J:CAS60 2.0 54.8 1.0
SG J:CAS60 2.3 43.8 1.0
CB J:CAS60 3.2 36.5 1.0
CA J:CAS60 3.4 35.0 1.0
CD2 J:LEU51 4.0 34.0 1.0
N J:CAS60 4.1 32.8 1.0
NE2 J:GLN49 4.4 41.4 1.0
O J:GLU59 4.5 33.2 1.0
C J:GLU59 4.6 34.4 1.0
C J:CAS60 4.7 34.0 1.0
CG J:LYS55 4.8 39.8 1.0
CB J:LYS55 4.8 36.3 1.0
CD J:GLN49 4.8 38.7 1.0
O J:CAS60 4.9 33.6 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 12:57:17 2024

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