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Arsenic in PDB 6fmj: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-N-(4-(4-Methylthiazol-5-Yl) Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3), PDB code: 6fmj was solved by P.Soares, X.Lucas, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 2.45
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.518, 93.518, 364.314, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 26.5

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

Arsenic binding site 1 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 1 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:60.8
occ:1.00
 AS A:CAS60 0.0 60.8 1.0
CE2 A:CAS60 2.0 61.9 1.0
CE1 A:CAS60 2.0 61.5 1.0
SG A:CAS60 2.3 49.3 1.0
CB A:CAS60 3.2 45.0 1.0
CA A:CAS60 3.4 44.4 1.0
CD2 A:LEU51 3.8 45.2 1.0
N A:CAS60 4.0 43.6 1.0
O A:GLU59 4.5 44.0 1.0
C A:GLU59 4.5 44.1 1.0
CB A:LYS55 4.5 43.9 1.0
CG A:LYS55 4.6 46.6 1.0
NE2 A:GLN49 4.7 57.2 1.0
C A:CAS60 4.7 43.5 1.0
O A:CAS60 4.9 44.6 1.0

Arsenic binding site 2 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 2 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:80.8
occ:1.00
 AS A:CAS89 0.0 80.8 1.0
CE1 A:CAS89 2.0 84.8 1.0
CE2 A:CAS89 2.0 78.4 1.0
SG A:CAS89 2.2 74.2 1.0
CB A:CAS89 3.1 64.9 1.0
CA A:CAS89 3.5 58.9 1.0
C A:CAS89 4.1 54.1 1.0
N A:ILE90 4.1 51.8 1.0
OE2 A:GLU91 4.6 62.2 1.0
O A:HOH290 4.7 55.4 1.0
N A:CAS89 4.8 56.3 1.0
O A:ILE90 4.8 49.2 1.0
C A:ILE90 4.9 48.5 1.0
O A:LEU88 4.9 59.4 1.0
O A:HOH266 4.9 67.0 1.0

Arsenic binding site 3 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 3 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:62.4
occ:1.00
 AS C:CAS77 0.0 62.4 1.0
CE2 C:CAS77 2.0 65.1 1.0
CE1 C:CAS77 2.0 61.6 1.0
SG C:CAS77 2.2 55.2 1.0
CB C:CAS77 3.1 48.9 1.0
CA C:CAS77 3.5 44.6 1.0
O C:THR105 4.2 46.5 1.0
CA C:GLY106 4.2 48.6 1.0
C C:CAS77 4.3 42.8 1.0
O K:HOH223 4.3 69.8 1.0
C C:THR105 4.4 48.4 1.0
N C:ASN78 4.4 42.2 1.0
N C:GLY106 4.5 49.0 1.0
CZ C:PHE148 4.5 62.9 1.0
CZ K:PHE109 4.6 58.0 1.0
CE K:MET45 4.7 74.5 1.0
N C:CAS77 4.7 42.3 1.0
O C:PHE76 5.0 42.1 1.0
CE2 C:PHE148 5.0 61.9 1.0

Arsenic binding site 4 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 4 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:57.9
occ:1.00
 AS D:CAS60 0.0 57.9 1.0
CE1 D:CAS60 2.0 59.0 1.0
CE2 D:CAS60 2.0 61.2 1.0
SG D:CAS60 2.2 53.5 1.0
CB D:CAS60 3.1 48.3 1.0
CA D:CAS60 3.4 45.9 1.0
N D:CAS60 4.0 45.2 1.0
CD2 D:LEU51 4.0 54.0 1.0
NE2 D:GLN49 4.4 57.0 1.0
C D:GLU59 4.5 45.6 1.0
O D:GLU59 4.5 45.8 1.0
C D:CAS60 4.6 44.3 1.0
CB D:LYS55 4.7 59.3 1.0
CG D:LYS55 4.8 61.3 1.0
CD D:GLN49 4.8 56.8 1.0
O D:CAS60 4.9 45.1 1.0
OE1 D:GLN49 5.0 55.2 1.0

Arsenic binding site 5 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 5 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:0.1
occ:1.00
 AS D:CAS89 0.0 0.1 1.0
CE1 D:CAS89 2.0 0.1 1.0
CE2 D:CAS89 2.0 0.1 1.0
SG D:CAS89 2.2 0.4 1.0
CB D:CAS89 3.1 95.5 1.0
CA D:CAS89 3.6 86.4 1.0
C D:CAS89 4.2 79.5 1.0
N D:ILE90 4.3 75.7 1.0
O D:LEU88 4.8 85.8 1.0
N D:CAS89 4.8 83.9 1.0
O D:HOH207 4.9 79.1 1.0

Arsenic binding site 6 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 6 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:64.8
occ:1.00
 AS F:CAS77 0.0 64.8 1.0
CE2 F:CAS77 2.0 66.4 1.0
CE1 F:CAS77 2.0 62.4 1.0
SG F:CAS77 2.2 56.0 1.0
CB F:CAS77 3.2 49.9 1.0
CA F:CAS77 3.6 46.0 1.0
CA F:GLY106 4.1 51.4 1.0
O F:THR105 4.2 45.9 1.0
C F:CAS77 4.3 43.3 1.0
N F:GLY106 4.3 51.8 1.0
C F:THR105 4.3 50.1 1.0
N F:ASN78 4.4 42.8 1.0
CE H:MET45 4.4 86.7 1.0
CZ F:PHE148 4.5 64.3 1.0
N F:CAS77 4.8 45.2 1.0

Arsenic binding site 7 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 7 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:66.5
occ:1.00
 AS G:CAS60 0.0 66.5 1.0
CE2 G:CAS60 2.0 67.8 1.0
CE1 G:CAS60 2.0 67.0 1.0
SG G:CAS60 2.2 63.4 1.0
CB G:CAS60 3.1 59.1 1.0
CA G:CAS60 3.4 58.5 1.0
NE2 G:GLN49 3.9 62.7 1.0
CD2 G:LEU51 3.9 64.3 1.0
N G:CAS60 4.2 59.0 1.0
C G:CAS60 4.6 57.4 1.0
O G:GLU59 4.6 63.0 1.0
CD G:GLN49 4.7 62.2 1.0
C G:GLU59 4.7 61.2 1.0
CB G:LYS55 4.7 67.0 1.0
O G:CAS60 4.8 56.7 1.0
CG G:LYS55 4.9 68.4 1.0
OE1 G:GLN49 4.9 62.0 1.0

Arsenic binding site 8 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 8 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:0.8
occ:1.00
 AS G:CAS89 0.0 0.8 1.0
CE2 G:CAS89 2.0 0.0 1.0
CE1 G:CAS89 2.0 0.7 1.0
SG G:CAS89 2.2 86.1 1.0
CB G:CAS89 3.1 70.6 1.0
CA G:CAS89 3.6 62.9 1.0
O G:HOH249 3.9 59.1 1.0
O G:HOH223 4.0 66.0 1.0
N G:ILE90 4.1 54.7 1.0
C G:CAS89 4.1 56.9 1.0
O G:ILE90 4.7 54.4 1.0
C G:ILE90 4.7 53.4 1.0
O G:HOH220 4.9 52.4 1.0
N G:CAS89 4.9 60.0 1.0

Arsenic binding site 9 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 9 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:56.0
occ:1.00
 AS I:CAS77 0.0 56.0 1.0
CE2 I:CAS77 2.0 56.1 1.0
CE1 I:CAS77 2.0 55.8 1.0
SG I:CAS77 2.2 48.6 1.0
CB I:CAS77 3.1 43.7 1.0
CA I:CAS77 3.5 40.1 1.0
CA I:GLY106 3.9 38.9 1.0
O I:THR105 4.0 38.0 1.0
C I:CAS77 4.1 38.8 1.0
N I:GLY106 4.1 39.0 1.0
C I:THR105 4.2 39.2 1.0
N I:ASN78 4.2 38.2 1.0
N I:CAS77 4.8 39.5 1.0
O I:CAS77 5.0 38.1 1.0

Arsenic binding site 10 out of 12 in 6fmj

Go back to Arsenic Binding Sites List in 6fmj
Arsenic binding site 10 out of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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)-1-((S)-2- Acetamidopropanethioyl)-4-Hydroxy-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:65.8
occ:1.00
 AS J:CAS60 0.0 65.8 1.0
CE1 J:CAS60 2.0 66.2 1.0
CE2 J:CAS60 2.0 65.4 1.0
SG J:CAS60 2.2 57.9 1.0
CB J:CAS60 3.2 49.3 1.0
CA J:CAS60 3.4 47.7 1.0
N J:CAS60 4.0 46.8 1.0
CD2 J:LEU51 4.1 47.0 1.0
O J:GLU59 4.4 48.2 1.0
NE2 J:GLN49 4.4 49.8 1.0
C J:GLU59 4.5 47.9 1.0
C J:CAS60 4.6 45.9 1.0
CB J:LYS55 4.7 48.3 1.0
CD J:GLN49 4.8 48.0 1.0
CG J:LYS55 4.8 50.6 1.0
O J:CAS60 4.9 45.5 1.0

Reference:

P.Soares, X.Lucas, A.Ciulli. Thioamide Substitution to Probe the Hydroxyproline Recognition of Vhl Ligands. Bioorg. Med. Chem. V. 26 2992 2018.
ISSN: ESSN 1464-3391
PubMed: 29650462
DOI: 10.1016/J.BMC.2018.03.034
Page generated: Wed Jul 10 13:17:19 2024

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