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Arsenic in PDB 6fmi: Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2), PDB code: 6fmi 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) 47.18 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 63.972, 69.863, 356.939, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.6

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) (pdb code 6fmi). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2), PDB code: 6fmi:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in 6fmi

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Arsenic binding site 1 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:75.0
occ:1.00
 AS A:CAS60 0.0 75.0 1.0
CE1 A:CAS60 2.0 76.4 1.0
CE2 A:CAS60 2.0 72.2 1.0
SG A:CAS60 2.2 61.7 1.0
CB A:CAS60 3.2 55.2 1.0
CA A:CAS60 3.5 51.4 1.0
CD2 A:LEU51 4.2 50.2 1.0
N A:CAS60 4.3 48.9 1.0
NE2 A:GLN49 4.6 66.6 1.0
O A:GLU59 4.7 52.0 1.0
C A:GLU59 4.7 52.4 1.0
C A:CAS60 4.7 50.3 1.0
CG A:LYS55 4.8 54.5 1.0
CD A:GLN49 4.9 63.9 1.0
O A:HOH226 4.9 59.5 1.0
CD A:LYS55 4.9 56.9 1.0
O A:CAS60 4.9 47.2 1.0

Arsenic binding site 2 out of 6 in 6fmi

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Arsenic binding site 2 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:0.1
occ:1.00
 AS A:CAS89 0.0 0.1 1.0
CE2 A:CAS89 2.0 99.1 1.0
CE1 A:CAS89 2.0 0.9 1.0
SG A:CAS89 2.2 89.0 1.0
CB A:CAS89 3.1 81.7 1.0
CA A:CAS89 3.5 72.6 1.0
N A:ILE90 3.8 60.6 1.0
C A:CAS89 3.9 63.6 1.0
C A:ILE90 4.5 57.5 1.0
O A:ILE90 4.6 58.3 1.0
CA A:ILE90 4.8 57.5 1.0
N A:GLU91 4.9 56.4 1.0
N A:CAS89 4.9 70.2 1.0
O A:CAS89 4.9 62.2 1.0
OE2 A:GLU91 4.9 73.2 1.0

Arsenic binding site 3 out of 6 in 6fmi

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Arsenic binding site 3 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:63.2
occ:1.00
 AS C:CAS77 0.0 63.2 1.0
CE1 C:CAS77 2.0 60.8 1.0
CE2 C:CAS77 2.0 63.8 1.0
SG C:CAS77 2.2 54.7 1.0
CB C:CAS77 3.2 46.1 1.0
CA C:CAS77 3.6 42.0 1.0
CA C:GLY106 4.1 42.0 1.0
O C:THR105 4.1 38.4 1.0
C C:CAS77 4.3 39.7 1.0
N C:GLY106 4.3 42.8 1.0
C C:THR105 4.4 41.3 1.0
N C:ASN78 4.4 39.1 1.0
N C:CAS77 4.8 40.4 1.0
NH2 C:ARG79 4.9 57.2 1.0
CZ C:ARG79 4.9 55.0 1.0
CE2 C:PHE148 5.0 44.3 1.0

Arsenic binding site 4 out of 6 in 6fmi

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Arsenic binding site 4 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:0.1
occ:1.00
 AS D:CAS60 0.0 0.1 1.0
CE2 D:CAS60 2.0 0.6 1.0
CE1 D:CAS60 2.0 0.9 1.0
SG D:CAS60 2.2 98.3 1.0
CB D:CAS60 3.2 89.6 1.0
CA D:CAS60 3.5 87.1 1.0
N D:CAS60 4.2 86.7 1.0
CD2 D:LEU51 4.2 89.9 1.0
O D:GLU59 4.6 90.1 1.0
C D:GLU59 4.6 88.5 1.0
NE2 D:GLN49 4.7 90.9 1.0
C D:CAS60 4.8 84.0 1.0

Arsenic binding site 5 out of 6 in 6fmi

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Arsenic binding site 5 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) 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 0.5 1.0
SG D:CAS89 2.2 0.5 1.0
CB D:CAS89 3.1 0.2 1.0
CA D:CAS89 3.5 0.3 1.0
N D:ILE90 3.6 0.3 1.0
C D:CAS89 3.8 0.3 1.0
O D:ILE90 3.9 1.0 1.0
C D:ILE90 4.1 0.3 1.0
OE2 D:GLU91 4.2 0.9 1.0
CA D:ILE90 4.5 0.6 1.0
N D:GLU91 4.7 99.5 1.0
O D:CAS89 4.8 0.9 1.0
N D:CAS89 4.9 0.1 1.0
CD D:GLU91 5.0 0.5 1.0

Arsenic binding site 6 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 6 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:74.4
occ:1.00
 AS F:CAS77 0.0 74.4 1.0
CE2 F:CAS77 2.0 75.5 1.0
CE1 F:CAS77 2.0 76.5 1.0
SG F:CAS77 2.2 66.2 1.0
CB F:CAS77 3.1 57.5 1.0
CA F:CAS77 3.5 52.5 1.0
CA F:GLY106 4.0 47.3 1.0
N F:GLY106 4.2 47.4 1.0
C F:CAS77 4.3 49.1 1.0
N F:ASN78 4.4 47.4 1.0
O F:THR105 4.4 44.3 1.0
C F:THR105 4.4 46.0 1.0
N F:CAS77 4.8 51.4 1.0
O F:PHE76 4.9 51.9 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: Mon Jul 7 00:36:43 2025

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