Arsenic in PDB 4w9e: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)
Protein crystallography data
The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4), PDB code: 4w9e
was solved by
M.S.Gadd,
P.Soares,
C.Galdeano,
I.Van Molle,
A.Ciulli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
93.10 /
2.60
|
Space group
|
P 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.097,
93.097,
364.436,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.6 /
26.1
|
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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4)
(pdb code 4w9e). 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-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4), PDB code: 4w9e:
Jump to Arsenic binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Arsenic binding site 1 out
of 12 in 4w9e
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Arsenic Binding Sites List in 4w9e
Arsenic binding site 1 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As60
b:77.8
occ:1.00
|
AS
|
A:CAS60
|
0.0
|
77.8
|
1.0
|
CE2
|
A:CAS60
|
2.0
|
71.6
|
1.0
|
CE1
|
A:CAS60
|
2.0
|
76.9
|
1.0
|
SG
|
A:CAS60
|
2.3
|
60.0
|
1.0
|
CB
|
A:CAS60
|
3.2
|
48.1
|
1.0
|
CA
|
A:CAS60
|
3.4
|
44.8
|
1.0
|
CD2
|
A:LEU51
|
3.8
|
39.4
|
1.0
|
N
|
A:CAS60
|
4.0
|
43.7
|
1.0
|
CB
|
A:LYS55
|
4.5
|
43.2
|
1.0
|
C
|
A:GLU59
|
4.5
|
45.7
|
1.0
|
NE2
|
A:GLN49
|
4.5
|
48.9
|
1.0
|
O
|
A:GLU59
|
4.6
|
44.8
|
1.0
|
CG
|
A:LYS55
|
4.6
|
46.5
|
1.0
|
C
|
A:CAS60
|
4.7
|
42.1
|
1.0
|
CD
|
A:GLN49
|
4.9
|
47.3
|
1.0
|
O
|
A:CAS60
|
5.0
|
41.7
|
1.0
|
OE1
|
A:GLN49
|
5.0
|
48.0
|
1.0
|
|
Arsenic binding site 2 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 2 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As89
b:95.3
occ:1.00
|
AS
|
A:CAS89
|
0.0
|
95.3
|
1.0
|
CE2
|
A:CAS89
|
2.0
|
95.3
|
1.0
|
CE1
|
A:CAS89
|
2.0
|
92.2
|
1.0
|
SG
|
A:CAS89
|
2.2
|
80.7
|
1.0
|
CB
|
A:CAS89
|
3.2
|
67.6
|
1.0
|
CA
|
A:CAS89
|
3.6
|
58.0
|
1.0
|
N
|
A:ILE90
|
3.9
|
52.5
|
1.0
|
C
|
A:CAS89
|
4.0
|
53.4
|
1.0
|
OE2
|
A:GLU91
|
4.3
|
77.4
|
1.0
|
C
|
A:ILE90
|
4.5
|
50.5
|
1.0
|
O
|
A:ILE90
|
4.5
|
50.0
|
1.0
|
N
|
A:GLU91
|
4.8
|
50.4
|
1.0
|
CA
|
A:ILE90
|
4.8
|
50.2
|
1.0
|
O
|
A:CAS89
|
5.0
|
51.5
|
1.0
|
|
Arsenic binding site 3 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 3 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:As77
b:70.8
occ:1.00
|
AS
|
C:CAS77
|
0.0
|
70.8
|
1.0
|
CE1
|
C:CAS77
|
2.0
|
69.4
|
1.0
|
CE2
|
C:CAS77
|
2.0
|
72.5
|
1.0
|
SG
|
C:CAS77
|
2.2
|
60.8
|
1.0
|
CB
|
C:CAS77
|
3.1
|
54.6
|
1.0
|
CA
|
C:CAS77
|
3.6
|
48.3
|
1.0
|
CE
|
K:MET45
|
4.2
|
86.7
|
1.0
|
CA
|
C:GLY106
|
4.3
|
49.8
|
1.0
|
O
|
C:THR105
|
4.3
|
45.6
|
1.0
|
CZ
|
C:PHE148
|
4.3
|
72.0
|
1.0
|
C
|
C:CAS77
|
4.4
|
46.1
|
1.0
|
N
|
C:GLY106
|
4.5
|
50.1
|
1.0
|
C
|
C:THR105
|
4.5
|
49.1
|
1.0
|
N
|
C:ASN78
|
4.6
|
44.2
|
1.0
|
CZ
|
K:PHE109
|
4.8
|
67.8
|
1.0
|
N
|
C:CAS77
|
4.9
|
45.1
|
1.0
|
O
|
C:PHE76
|
4.9
|
46.7
|
1.0
|
SD
|
K:MET45
|
5.0
|
87.1
|
1.0
|
CE2
|
C:PHE148
|
5.0
|
71.0
|
1.0
|
|
Arsenic binding site 4 out
of 12 in 4w9e
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Arsenic Binding Sites List in 4w9e
Arsenic binding site 4 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As60
b:65.2
occ:1.00
|
AS
|
D:CAS60
|
0.0
|
65.2
|
1.0
|
CE1
|
D:CAS60
|
2.0
|
65.6
|
1.0
|
CE2
|
D:CAS60
|
2.0
|
68.6
|
1.0
|
SG
|
D:CAS60
|
2.2
|
57.5
|
1.0
|
CB
|
D:CAS60
|
3.2
|
48.5
|
1.0
|
CA
|
D:CAS60
|
3.4
|
44.1
|
1.0
|
CD2
|
D:LEU51
|
4.0
|
48.1
|
1.0
|
N
|
D:CAS60
|
4.1
|
43.0
|
1.0
|
O
|
D:GLU59
|
4.4
|
44.3
|
1.0
|
C
|
D:GLU59
|
4.5
|
44.4
|
1.0
|
CB
|
D:LYS55
|
4.6
|
57.0
|
1.0
|
NE2
|
D:GLN49
|
4.6
|
47.5
|
1.0
|
CG
|
D:LYS55
|
4.6
|
57.8
|
1.0
|
C
|
D:CAS60
|
4.7
|
42.8
|
1.0
|
CD
|
D:GLN49
|
4.9
|
46.9
|
1.0
|
O
|
D:CAS60
|
4.9
|
42.4
|
1.0
|
OE1
|
D:GLN49
|
4.9
|
46.1
|
1.0
|
|
Arsenic binding site 5 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 5 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As89
b:0.4
occ:1.00
|
AS
|
D:CAS89
|
0.0
|
0.4
|
1.0
|
CE2
|
D:CAS89
|
2.0
|
0.2
|
1.0
|
CE1
|
D:CAS89
|
2.0
|
0.4
|
1.0
|
SG
|
D:CAS89
|
2.2
|
0.6
|
1.0
|
CB
|
D:CAS89
|
3.2
|
90.3
|
1.0
|
CA
|
D:CAS89
|
3.7
|
80.3
|
1.0
|
N
|
D:ILE90
|
4.1
|
70.8
|
1.0
|
C
|
D:CAS89
|
4.2
|
75.8
|
1.0
|
O
|
D:ILE90
|
4.6
|
59.4
|
1.0
|
C
|
D:ILE90
|
4.7
|
62.9
|
1.0
|
N
|
D:GLU91
|
5.0
|
67.4
|
1.0
|
N
|
D:CAS89
|
5.0
|
75.0
|
1.0
|
|
Arsenic binding site 6 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 6 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:As77
b:67.0
occ:1.00
|
AS
|
F:CAS77
|
0.0
|
67.0
|
1.0
|
CE1
|
F:CAS77
|
2.0
|
67.3
|
1.0
|
CE2
|
F:CAS77
|
2.0
|
69.2
|
1.0
|
SG
|
F:CAS77
|
2.2
|
56.7
|
1.0
|
CB
|
F:CAS77
|
3.2
|
50.3
|
1.0
|
CA
|
F:CAS77
|
3.7
|
47.0
|
1.0
|
CE
|
H:MET45
|
4.1
|
83.3
|
1.0
|
CA
|
F:GLY106
|
4.2
|
54.1
|
1.0
|
CZ
|
F:PHE148
|
4.2
|
63.9
|
1.0
|
O
|
F:THR105
|
4.3
|
43.1
|
1.0
|
N
|
F:GLY106
|
4.4
|
53.8
|
1.0
|
C
|
F:THR105
|
4.5
|
50.5
|
1.0
|
C
|
F:CAS77
|
4.5
|
44.5
|
1.0
|
N
|
F:ASN78
|
4.7
|
43.3
|
1.0
|
CG
|
H:MET45
|
4.7
|
82.3
|
1.0
|
SD
|
H:MET45
|
4.8
|
84.8
|
1.0
|
CE2
|
F:PHE148
|
4.9
|
63.9
|
1.0
|
N
|
F:CAS77
|
5.0
|
45.5
|
1.0
|
|
Arsenic binding site 7 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 7 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As60
b:69.9
occ:1.00
|
AS
|
G:CAS60
|
0.0
|
69.9
|
1.0
|
CE1
|
G:CAS60
|
2.0
|
72.5
|
1.0
|
CE2
|
G:CAS60
|
2.0
|
70.0
|
1.0
|
SG
|
G:CAS60
|
2.2
|
60.6
|
1.0
|
CB
|
G:CAS60
|
3.2
|
55.6
|
1.0
|
CA
|
G:CAS60
|
3.4
|
52.6
|
1.0
|
CD2
|
G:LEU51
|
4.0
|
55.1
|
1.0
|
N
|
G:CAS60
|
4.0
|
52.1
|
1.0
|
NE2
|
G:GLN49
|
4.4
|
48.8
|
1.0
|
CB
|
G:LYS55
|
4.6
|
66.3
|
1.0
|
C
|
G:GLU59
|
4.6
|
56.5
|
1.0
|
CG
|
G:LYS55
|
4.6
|
69.8
|
1.0
|
C
|
G:CAS60
|
4.6
|
53.6
|
1.0
|
O
|
G:GLU59
|
4.7
|
56.2
|
1.0
|
CD
|
G:GLN49
|
4.8
|
48.5
|
1.0
|
O
|
G:CAS60
|
4.9
|
54.3
|
1.0
|
OE1
|
G:GLN49
|
5.0
|
49.1
|
1.0
|
|
Arsenic binding site 8 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 8 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As89
b:99.5
occ:1.00
|
AS
|
G:CAS89
|
0.0
|
99.5
|
1.0
|
CE1
|
G:CAS89
|
2.0
|
93.2
|
1.0
|
CE2
|
G:CAS89
|
2.0
|
0.4
|
1.0
|
SG
|
G:CAS89
|
2.2
|
72.4
|
1.0
|
CB
|
G:CAS89
|
3.1
|
60.9
|
1.0
|
CA
|
G:CAS89
|
3.8
|
52.6
|
1.0
|
C
|
G:CAS89
|
4.3
|
49.1
|
1.0
|
N
|
G:ILE90
|
4.3
|
46.5
|
1.0
|
O
|
G:HOH213
|
4.8
|
58.1
|
1.0
|
|
Arsenic binding site 9 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 9 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:As77
b:60.0
occ:1.00
|
AS
|
I:CAS77
|
0.0
|
60.0
|
1.0
|
CE2
|
I:CAS77
|
2.0
|
63.1
|
1.0
|
CE1
|
I:CAS77
|
2.0
|
63.0
|
1.0
|
SG
|
I:CAS77
|
2.2
|
55.0
|
1.0
|
CB
|
I:CAS77
|
3.1
|
45.6
|
1.0
|
CA
|
I:CAS77
|
3.6
|
40.1
|
1.0
|
O
|
I:THR105
|
4.0
|
41.8
|
1.0
|
CA
|
I:GLY106
|
4.0
|
42.3
|
1.0
|
C
|
I:THR105
|
4.2
|
42.2
|
1.0
|
N
|
I:GLY106
|
4.3
|
41.7
|
1.0
|
C
|
I:CAS77
|
4.3
|
38.5
|
1.0
|
N
|
I:ASN78
|
4.4
|
38.3
|
1.0
|
N
|
I:CAS77
|
4.8
|
39.8
|
1.0
|
CZ
|
I:PHE148
|
4.9
|
58.7
|
1.0
|
CE2
|
I:PHE148
|
4.9
|
59.1
|
1.0
|
|
Arsenic binding site 10 out
of 12 in 4w9e
Go back to
Arsenic Binding Sites List in 4w9e
Arsenic binding site 10 out
of 12 in the Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Thiazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 4) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:As60
b:75.5
occ:1.00
|
AS
|
J:CAS60
|
0.0
|
75.5
|
1.0
|
CE2
|
J:CAS60
|
2.0
|
73.6
|
1.0
|
CE1
|
J:CAS60
|
2.0
|
73.5
|
1.0
|
SG
|
J:CAS60
|
2.3
|
59.2
|
1.0
|
CB
|
J:CAS60
|
3.3
|
47.9
|
1.0
|
CA
|
J:CAS60
|
3.4
|
43.9
|
1.0
|
CD2
|
J:LEU51
|
4.0
|
43.6
|
1.0
|
N
|
J:CAS60
|
4.1
|
42.0
|
1.0
|
NE2
|
J:GLN49
|
4.4
|
44.7
|
1.0
|
O
|
J:GLU59
|
4.5
|
47.4
|
1.0
|
C
|
J:GLU59
|
4.6
|
45.0
|
1.0
|
CB
|
J:LYS55
|
4.6
|
45.5
|
1.0
|
CG
|
J:LYS55
|
4.6
|
48.5
|
1.0
|
C
|
J:CAS60
|
4.7
|
41.5
|
1.0
|
CD
|
J:GLN49
|
4.9
|
42.7
|
1.0
|
O
|
J:CAS60
|
4.9
|
39.5
|
1.0
|
|
Reference:
C.Galdeano,
M.S.Gadd,
P.Soares,
S.Scaffidi,
I.Van Molle,
I.Birced,
S.Hewitt,
D.M.Dias,
A.Ciulli.
Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction Between the Von Hippel-Lindau (Vhl) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (Hif) Alpha Subunit with in Vitro Nanomolar Affinities. J.Med.Chem. V. 57 8657 2014.
ISSN: ISSN 0022-2623
PubMed: 25166285
DOI: 10.1021/JM5011258
Page generated: Wed Jul 10 12:30:10 2024
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