Arsenic in PDB 6fmk: 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4), PDB code: 6fmk
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)
|
47.38 /
2.75
|
Space group
|
P 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.768,
94.768,
365.819,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
26
|
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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Thioxopropan-2-Yl)Acetamide (Ligand 4)
(pdb code 6fmk). 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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Thioxopropan-2-Yl)Acetamide (Ligand 4), PDB code: 6fmk:
Jump to Arsenic binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Arsenic binding site 1 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 1 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As60
b:78.5
occ:1.00
|
AS
|
A:CAS60
|
0.0
|
78.5
|
1.0
|
CE2
|
A:CAS60
|
2.0
|
73.0
|
1.0
|
CE1
|
A:CAS60
|
2.0
|
76.7
|
1.0
|
SG
|
A:CAS60
|
2.3
|
61.6
|
1.0
|
CB
|
A:CAS60
|
3.2
|
52.2
|
1.0
|
CA
|
A:CAS60
|
3.5
|
50.4
|
1.0
|
CD2
|
A:LEU51
|
3.9
|
48.5
|
1.0
|
N
|
A:CAS60
|
4.0
|
48.6
|
1.0
|
O
|
A:GLU59
|
4.3
|
50.7
|
1.0
|
C
|
A:GLU59
|
4.4
|
49.7
|
1.0
|
CB
|
A:LYS55
|
4.5
|
49.3
|
1.0
|
CG
|
A:LYS55
|
4.6
|
52.6
|
1.0
|
C
|
A:CAS60
|
4.7
|
49.0
|
1.0
|
NE2
|
A:GLN49
|
5.0
|
59.9
|
1.0
|
|
Arsenic binding site 2 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 2 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As89
b:0.3
occ:1.00
|
AS
|
A:CAS89
|
0.0
|
0.3
|
1.0
|
CE1
|
A:CAS89
|
2.0
|
0.1
|
1.0
|
CE2
|
A:CAS89
|
2.0
|
99.2
|
1.0
|
SG
|
A:CAS89
|
2.2
|
88.0
|
1.0
|
CB
|
A:CAS89
|
3.1
|
78.2
|
1.0
|
CA
|
A:CAS89
|
3.5
|
70.6
|
1.0
|
C
|
A:CAS89
|
4.1
|
64.3
|
1.0
|
N
|
A:ILE90
|
4.2
|
61.5
|
1.0
|
OE2
|
A:GLU91
|
4.4
|
77.5
|
1.0
|
N
|
A:CAS89
|
4.8
|
67.8
|
1.0
|
O
|
A:LEU88
|
4.8
|
69.9
|
1.0
|
C
|
A:ILE90
|
5.0
|
59.1
|
1.0
|
O
|
A:ILE90
|
5.0
|
60.5
|
1.0
|
|
Arsenic binding site 3 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 3 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:As77
b:74.9
occ:1.00
|
AS
|
C:CAS77
|
0.0
|
74.9
|
1.0
|
CE1
|
C:CAS77
|
2.0
|
73.0
|
1.0
|
CE2
|
C:CAS77
|
2.0
|
77.4
|
1.0
|
SG
|
C:CAS77
|
2.2
|
62.2
|
1.0
|
CB
|
C:CAS77
|
3.1
|
57.1
|
1.0
|
CA
|
C:CAS77
|
3.7
|
52.4
|
1.0
|
O
|
C:THR105
|
4.3
|
59.9
|
1.0
|
CA
|
C:GLY106
|
4.4
|
60.4
|
1.0
|
C
|
C:CAS77
|
4.4
|
49.1
|
1.0
|
CZ
|
C:PHE148
|
4.5
|
79.2
|
1.0
|
C
|
C:THR105
|
4.6
|
60.7
|
1.0
|
N
|
C:GLY106
|
4.6
|
62.0
|
1.0
|
N
|
C:ASN78
|
4.6
|
47.9
|
1.0
|
CE2
|
C:PHE148
|
4.7
|
77.0
|
1.0
|
CE
|
K:MET45
|
4.8
|
86.2
|
1.0
|
CZ
|
K:PHE109
|
4.9
|
62.7
|
1.0
|
N
|
C:CAS77
|
5.0
|
49.9
|
1.0
|
|
Arsenic binding site 4 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 4 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As60
b:68.8
occ:1.00
|
AS
|
D:CAS60
|
0.0
|
68.8
|
1.0
|
CE1
|
D:CAS60
|
2.0
|
70.0
|
1.0
|
CE2
|
D:CAS60
|
2.0
|
71.8
|
1.0
|
SG
|
D:CAS60
|
2.2
|
60.3
|
1.0
|
CB
|
D:CAS60
|
3.2
|
55.6
|
1.0
|
CA
|
D:CAS60
|
3.5
|
52.7
|
1.0
|
CD2
|
D:LEU51
|
4.1
|
62.5
|
1.0
|
N
|
D:CAS60
|
4.2
|
52.2
|
1.0
|
NE2
|
D:GLN49
|
4.5
|
57.4
|
1.0
|
C
|
D:GLU59
|
4.7
|
53.1
|
1.0
|
O
|
D:GLU59
|
4.7
|
52.7
|
1.0
|
CD
|
D:GLN49
|
4.8
|
56.7
|
1.0
|
C
|
D:CAS60
|
4.8
|
50.0
|
1.0
|
OE1
|
D:GLN49
|
4.9
|
53.7
|
1.0
|
|
Arsenic binding site 5 out
of 12 in 6fmk
Go back to
Arsenic Binding Sites List in 6fmk
Arsenic binding site 5 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4) 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
|
0.5
|
1.0
|
CE2
|
D:CAS89
|
2.0
|
0.5
|
1.0
|
SG
|
D:CAS89
|
2.2
|
0.9
|
1.0
|
CB
|
D:CAS89
|
3.1
|
0.7
|
1.0
|
CA
|
D:CAS89
|
3.5
|
0.5
|
1.0
|
C
|
D:CAS89
|
4.2
|
96.1
|
1.0
|
N
|
D:ILE90
|
4.2
|
89.7
|
1.0
|
OE2
|
D:GLU91
|
4.2
|
0.8
|
1.0
|
N
|
D:CAS89
|
4.8
|
0.4
|
1.0
|
O
|
D:ILE90
|
4.8
|
79.3
|
1.0
|
O
|
D:LEU88
|
4.9
|
0.4
|
1.0
|
C
|
D:ILE90
|
4.9
|
81.6
|
1.0
|
|
Arsenic binding site 6 out
of 12 in 6fmk
Go back to
Arsenic Binding Sites List in 6fmk
Arsenic binding site 6 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:As77
b:82.1
occ:1.00
|
AS
|
F:CAS77
|
0.0
|
82.1
|
1.0
|
CE2
|
F:CAS77
|
2.0
|
84.2
|
1.0
|
CE1
|
F:CAS77
|
2.0
|
79.2
|
1.0
|
SG
|
F:CAS77
|
2.2
|
69.7
|
1.0
|
CB
|
F:CAS77
|
3.2
|
63.2
|
1.0
|
CA
|
F:CAS77
|
3.7
|
58.1
|
1.0
|
O
|
F:THR105
|
4.2
|
63.0
|
1.0
|
CA
|
F:GLY106
|
4.2
|
65.0
|
1.0
|
C
|
F:THR105
|
4.4
|
65.1
|
1.0
|
C
|
F:CAS77
|
4.4
|
54.4
|
1.0
|
N
|
F:GLY106
|
4.4
|
66.2
|
1.0
|
N
|
F:ASN78
|
4.6
|
54.5
|
1.0
|
CZ
|
F:PHE148
|
4.7
|
79.1
|
1.0
|
CE2
|
F:PHE148
|
4.8
|
77.2
|
1.0
|
N
|
F:CAS77
|
5.0
|
56.2
|
1.0
|
|
Arsenic binding site 7 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 7 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As60
b:87.2
occ:1.00
|
AS
|
G:CAS60
|
0.0
|
87.2
|
1.0
|
CE1
|
G:CAS60
|
2.0
|
87.1
|
1.0
|
CE2
|
G:CAS60
|
2.0
|
89.0
|
1.0
|
SG
|
G:CAS60
|
2.2
|
82.8
|
1.0
|
CB
|
G:CAS60
|
3.2
|
77.7
|
1.0
|
CA
|
G:CAS60
|
3.5
|
76.7
|
1.0
|
NE2
|
G:GLN49
|
3.9
|
79.6
|
1.0
|
CD2
|
G:LEU51
|
4.0
|
83.4
|
1.0
|
N
|
G:CAS60
|
4.3
|
77.8
|
1.0
|
CD
|
G:GLN49
|
4.6
|
79.2
|
1.0
|
C
|
G:CAS60
|
4.7
|
74.1
|
1.0
|
CG
|
G:LYS55
|
4.8
|
87.7
|
1.0
|
CB
|
G:LYS55
|
4.8
|
85.5
|
1.0
|
O
|
G:CAS60
|
4.8
|
72.8
|
1.0
|
C
|
G:GLU59
|
4.9
|
79.7
|
1.0
|
OE1
|
G:GLN49
|
4.9
|
78.6
|
1.0
|
O
|
G:GLU59
|
5.0
|
80.7
|
1.0
|
|
Arsenic binding site 8 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 8 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As89
b:0.7
occ:1.00
|
AS
|
G:CAS89
|
0.0
|
0.7
|
1.0
|
CE2
|
G:CAS89
|
2.0
|
0.8
|
1.0
|
CE1
|
G:CAS89
|
2.0
|
0.1
|
1.0
|
SG
|
G:CAS89
|
2.2
|
0.5
|
1.0
|
CB
|
G:CAS89
|
3.1
|
0.6
|
1.0
|
CA
|
G:CAS89
|
3.6
|
93.0
|
1.0
|
N
|
G:ILE90
|
4.0
|
80.8
|
1.0
|
C
|
G:CAS89
|
4.2
|
86.3
|
1.0
|
C
|
G:ILE90
|
4.7
|
74.3
|
1.0
|
O
|
G:ILE90
|
4.8
|
72.5
|
1.0
|
N
|
G:CAS89
|
4.9
|
88.1
|
1.0
|
N
|
G:GLU91
|
4.9
|
73.9
|
1.0
|
CA
|
G:ILE90
|
5.0
|
77.1
|
1.0
|
|
Arsenic binding site 9 out
of 12 in 6fmk
Go back to
Arsenic Binding Sites List in 6fmk
Arsenic binding site 9 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:As77
b:68.2
occ:1.00
|
AS
|
I:CAS77
|
0.0
|
68.2
|
1.0
|
CE2
|
I:CAS77
|
2.0
|
65.4
|
1.0
|
CE1
|
I:CAS77
|
2.0
|
71.8
|
1.0
|
SG
|
I:CAS77
|
2.2
|
62.1
|
1.0
|
CB
|
I:CAS77
|
3.2
|
53.1
|
1.0
|
CA
|
I:CAS77
|
3.6
|
48.6
|
1.0
|
O
|
I:THR105
|
3.9
|
50.8
|
1.0
|
CA
|
I:GLY106
|
4.1
|
50.9
|
1.0
|
C
|
I:THR105
|
4.2
|
52.3
|
1.0
|
C
|
I:CAS77
|
4.2
|
46.6
|
1.0
|
N
|
I:GLY106
|
4.3
|
53.0
|
1.0
|
N
|
I:ASN78
|
4.4
|
47.3
|
1.0
|
N
|
I:CAS77
|
4.9
|
47.3
|
1.0
|
|
Arsenic binding site 10 out
of 12 in 6fmk
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Arsenic Binding Sites List in 6fmk
Arsenic binding site 10 out
of 12 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- Thioxopropan-2-Yl)Acetamide (Ligand 4)
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 N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Thioxopropan-2-Yl)Acetamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:As60
b:77.5
occ:1.00
|
AS
|
J:CAS60
|
0.0
|
77.5
|
1.0
|
CE2
|
J:CAS60
|
2.0
|
77.5
|
1.0
|
CE1
|
J:CAS60
|
2.0
|
80.0
|
1.0
|
SG
|
J:CAS60
|
2.3
|
68.7
|
1.0
|
CB
|
J:CAS60
|
3.2
|
59.1
|
1.0
|
CA
|
J:CAS60
|
3.5
|
56.8
|
1.0
|
CD2
|
J:LEU51
|
4.0
|
58.2
|
1.0
|
N
|
J:CAS60
|
4.2
|
55.6
|
1.0
|
NE2
|
J:GLN49
|
4.5
|
55.1
|
1.0
|
CG
|
J:LYS55
|
4.7
|
59.4
|
1.0
|
O
|
J:GLU59
|
4.7
|
58.6
|
1.0
|
C
|
J:CAS60
|
4.7
|
54.1
|
1.0
|
C
|
J:GLU59
|
4.7
|
56.9
|
1.0
|
CB
|
J:LYS55
|
4.7
|
56.5
|
1.0
|
CD
|
J:GLN49
|
4.8
|
54.1
|
1.0
|
O
|
J:CAS60
|
4.9
|
54.2
|
1.0
|
OE1
|
J:GLN49
|
4.9
|
53.4
|
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 13:17:18 2024
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