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Arsenic in PDB 8cqe: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37), PDB code: 8cqe was solved by R.Casement, L.Phuong Vu, A.Ciulli, M.Gutschow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.05 / 2.85
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.971, 92.971, 362.047, 90, 90, 90
R / Rfree (%) 24.3 / 29.7

Other elements in 8cqe:

The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) also contains other interesting chemical elements:

Fluorine (F) 8 atoms

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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) (pdb code 8cqe). 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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37), PDB code: 8cqe:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:89.2
occ:1.00
 AS A:CAS60 0.0 89.2 1.0
CE1 A:CAS60 2.0 61.4 1.0
CE2 A:CAS60 2.0 46.5 1.0
SG A:CAS60 2.2 72.9 1.0
CB A:CAS60 3.2 45.9 1.0
CA A:CAS60 3.6 50.7 1.0
OE1 A:GLN49 4.0 40.3 1.0
N A:CAS60 4.3 47.1 1.0
CG A:LEU51 4.3 62.4 1.0
CG A:LYS55 4.6 52.8 1.0
CB A:LYS55 4.6 47.5 1.0
CD A:GLN49 4.6 41.2 1.0
O A:GLU59 4.7 55.0 1.0
CD1 A:LEU51 4.7 56.1 1.0
C A:GLU59 4.8 45.4 1.0
CD A:LYS55 4.8 50.2 1.0
C A:CAS60 4.8 49.4 1.0
CA A:LEU51 5.0 50.5 1.0

Arsenic binding site 2 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:134.6
occ:1.00
 AS A:CAS89 0.0 134.6 1.0
CE2 A:CAS89 2.0 81.0 1.0
CE1 A:CAS89 2.0 78.0 1.0
SG A:CAS89 2.2 77.1 1.0
CB A:CAS89 3.1 55.6 1.0
CA A:CAS89 3.7 54.1 1.0
C A:CAS89 4.2 60.7 1.0
N A:ILE90 4.2 47.2 1.0
OE2 A:GLU91 4.9 52.9 1.0
C A:ILE90 4.9 45.0 1.0
O A:ILE90 4.9 39.5 1.0
N A:CAS89 5.0 46.4 1.0

Arsenic binding site 3 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:62.7
occ:1.00
 AS C:CAS77 0.0 62.7 1.0
CE2 C:CAS77 2.0 49.3 1.0
CE1 C:CAS77 2.0 49.7 1.0
SG C:CAS77 2.2 75.7 1.0
CB C:CAS77 3.1 40.5 1.0
CA C:CAS77 3.6 40.7 1.0
CA C:GLY106 4.1 45.3 1.0
O C:THR105 4.3 46.3 1.0
C C:CAS77 4.3 44.1 1.0
N C:GLY106 4.4 54.4 1.0
N C:ASN78 4.5 41.2 1.0
C C:THR105 4.5 45.5 1.0
CE2 C:PHE148 4.7 52.5 1.0
N C:CAS77 4.8 38.9 1.0
O C:PHE76 5.0 38.0 1.0

Arsenic binding site 4 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:88.5
occ:1.00
 AS D:CAS60 0.0 88.5 1.0
CE1 D:CAS60 2.0 53.2 1.0
CE2 D:CAS60 2.0 47.4 1.0
SG D:CAS60 2.2 61.3 1.0
CB D:CAS60 3.1 34.0 1.0
CA D:CAS60 3.4 33.4 1.0
CD2 D:LEU51 4.1 36.7 1.0
N D:CAS60 4.1 36.7 1.0
CB D:LYS55 4.3 29.5 1.0
NE2 D:GLN49 4.4 48.8 1.0
CG D:LYS55 4.4 39.7 1.0
O D:GLU59 4.4 38.7 1.0
C D:GLU59 4.5 39.0 1.0
OE1 D:GLN49 4.6 68.5 1.0
C D:CAS60 4.7 33.5 1.0
O D:CAS60 4.9 34.0 1.0
CD D:GLN49 4.9 53.4 1.0

Arsenic binding site 5 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:93.4
occ:1.00
 AS D:CAS89 0.0 93.4 1.0
CE1 D:CAS89 2.0 72.9 1.0
CE2 D:CAS89 2.0 58.5 1.0
SG D:CAS89 2.2 69.7 1.0
CB D:CAS89 3.1 38.1 1.0
CA D:CAS89 3.6 39.9 1.0
C D:CAS89 4.2 37.0 1.0
N D:ILE90 4.3 32.1 1.0
N D:CAS89 4.9 32.5 1.0

Arsenic binding site 6 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:63.7
occ:1.00
 AS F:CAS77 0.0 63.7 1.0
CE2 F:CAS77 2.0 49.3 1.0
CE1 F:CAS77 2.0 40.6 1.0
SG F:CAS77 2.2 53.4 1.0
CB F:CAS77 3.1 31.0 1.0
CA F:CAS77 3.6 30.6 1.0
CA F:GLY106 3.9 37.0 1.0
O F:THR105 4.2 40.2 1.0
N F:GLY106 4.2 45.8 1.0
C F:CAS77 4.2 36.5 1.0
C F:THR105 4.3 42.5 1.0
N F:ASN78 4.4 34.6 1.0
N F:CAS77 4.8 24.0 1.0
O F:PHE76 5.0 30.6 1.0

Arsenic binding site 7 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:99.0
occ:1.00
 AS G:CAS60 0.0 99.0 1.0
CE1 G:CAS60 2.0 56.0 1.0
CE2 G:CAS60 2.0 49.4 1.0
SG G:CAS60 2.2 74.8 1.0
CB G:CAS60 3.1 30.9 1.0
CA G:CAS60 3.4 39.0 1.0
CD2 G:LEU51 3.8 42.7 1.0
N G:CAS60 4.2 40.8 1.0
NE2 G:GLN49 4.2 40.8 1.0
O G:GLU59 4.5 44.1 1.0
CD G:LYS55 4.6 46.5 1.0
C G:GLU59 4.6 41.0 1.0
C G:CAS60 4.7 42.9 1.0
CB G:LEU51 4.8 47.4 1.0
CA G:LEU51 4.8 52.9 1.0
CG G:LEU51 4.8 39.1 1.0
CD G:GLN49 4.9 48.4 1.0
CB G:LYS55 4.9 37.8 1.0
O G:CAS60 4.9 53.2 1.0

Arsenic binding site 8 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:117.2
occ:1.00
 AS G:CAS89 0.0 117.2 1.0
CE1 G:CAS89 2.0 57.7 1.0
CE2 G:CAS89 2.0 75.1 1.0
SG G:CAS89 2.2 69.5 1.0
CB G:CAS89 3.1 48.0 1.0
CA G:CAS89 3.6 43.1 1.0
N G:ILE90 4.2 52.9 1.0
C G:CAS89 4.2 51.9 1.0
N G:CAS89 4.9 45.4 1.0
C G:ILE90 4.9 50.5 1.0
O G:ILE90 4.9 47.1 1.0

Arsenic binding site 9 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As77

b:66.1
occ:1.00
 AS I:CAS77 0.0 66.1 1.0
CE2 I:CAS77 2.0 52.5 1.0
CE1 I:CAS77 2.0 60.7 1.0
SG I:CAS77 2.2 47.1 1.0
CB I:CAS77 3.1 38.3 1.0
CA I:CAS77 4.0 36.3 1.0
CZ I:PHE148 4.0 41.6 1.0
CA I:GLY106 4.2 35.6 1.0
SD E:MET45 4.4 61.7 1.0
NH1 I:ARG79 4.4 51.3 1.0
N I:GLY106 4.6 33.7 1.0
CZ I:ARG79 4.7 47.3 1.0
O I:THR105 4.7 25.0 1.0
CE1 I:PHE148 4.7 35.5 1.0
NH2 I:ARG79 4.7 44.6 1.0
C I:CAS77 4.7 33.1 1.0
C I:THR105 4.8 32.6 1.0
CG E:MET45 4.8 34.4 1.0
CE2 I:PHE148 4.9 38.6 1.0
CE E:MET45 5.0 24.7 1.0
N I:ASN78 5.0 26.7 1.0

Arsenic binding site 10 out of 12 in 8cqe

Go back to Arsenic Binding Sites List in 8cqe
Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2-(1-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37)


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-Fluorocyclopropane- 1-Carboxamido)-3,3-Dimethylbutanoyl)-4-Hydroxy-N-((S)-1-(2-Methyl-4- (4-Methylthiazol-5-Yl)Phenyl)Ethyl)Pyrrolidine-2-Carboxamide (Compound 37) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As60

b:85.5
occ:1.00
 AS J:CAS60 0.0 85.5 1.0
CE2 J:CAS60 2.0 57.3 1.0
CE1 J:CAS60 2.0 47.2 1.0
SG J:CAS60 2.2 55.8 1.0
CB J:CAS60 3.1 52.3 1.0
CA J:CAS60 3.5 45.2 1.0
CD2 J:LEU51 3.9 44.1 1.0
NE2 J:GLN49 4.2 40.2 1.0
N J:CAS60 4.2 37.6 1.0
O J:GLU59 4.5 48.3 1.0
CG J:LYS55 4.5 59.3 1.0
NZ J:LYS55 4.5 59.8 1.0
CB J:LYS55 4.6 55.6 1.0
C J:GLU59 4.6 40.2 1.0
C J:CAS60 4.7 47.6 1.0
O J:CAS60 4.8 50.1 1.0
CD J:GLN49 4.9 50.3 1.0
CA J:LEU51 4.9 65.2 1.0

Reference:

L.P.Vu, C.J.Diehl, R.Casement, A.G.Bond, C.Steinebach, N.Strasek, A.Bricelj, A.Perdih, G.Schnakenburg, I.Sosic, A.Ciulli, M.Gutschow. Expanding the Structural Diversity at the Phenylene Core of Ligands For the Von Hippel-Lindau E3 Ubiquitin Ligase: Development of Highly Potent Hypoxia-Inducible Factor-1 Alpha Stabilizers. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37708384
DOI: 10.1021/ACS.JMEDCHEM.3C00434
Page generated: Wed Jul 10 13:58:55 2024

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