Arsenic in PDB 4w9c: Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)
Protein crystallography data
The structure of Pvhl:Elob:Eloc in Complex with (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2), PDB code: 4w9c
was solved by
M.S.Gadd,
S.Hewitt,
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)
|
93.78 /
2.20
|
Space group
|
P 41 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.779,
93.779,
366.034,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
20.6 /
25.1
|
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)
(pdb code 4w9c). 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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2), PDB code: 4w9c:
Jump to Arsenic binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Arsenic binding site 1 out
of 12 in 4w9c
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Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As60
b:55.7
occ:1.00
|
AS
|
A:CAS60
|
0.0
|
55.7
|
1.0
|
CE2
|
A:CAS60
|
2.0
|
55.9
|
1.0
|
CE1
|
A:CAS60
|
2.0
|
56.8
|
1.0
|
SG
|
A:CAS60
|
2.3
|
38.4
|
1.0
|
CB
|
A:CAS60
|
3.2
|
31.2
|
1.0
|
CA
|
A:CAS60
|
3.4
|
28.5
|
1.0
|
CD2
|
A:LEU51
|
3.8
|
31.5
|
1.0
|
N
|
A:CAS60
|
4.0
|
27.7
|
1.0
|
O
|
A:GLU59
|
4.4
|
27.6
|
1.0
|
NE2
|
A:GLN49
|
4.5
|
37.6
|
1.0
|
C
|
A:GLU59
|
4.5
|
27.5
|
1.0
|
CB
|
A:LYS55
|
4.5
|
27.9
|
1.0
|
CG
|
A:LYS55
|
4.6
|
30.4
|
1.0
|
C
|
A:CAS60
|
4.7
|
28.8
|
1.0
|
O
|
A:CAS60
|
5.0
|
29.9
|
1.0
|
CD
|
A:GLN49
|
5.0
|
36.4
|
1.0
|
|
Arsenic binding site 2 out
of 12 in 4w9c
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Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:As89
b:67.5
occ:1.00
|
AS
|
A:CAS89
|
0.0
|
67.5
|
1.0
|
CE1
|
A:CAS89
|
2.0
|
69.2
|
1.0
|
CE2
|
A:CAS89
|
2.0
|
69.7
|
1.0
|
SG
|
A:CAS89
|
2.2
|
53.6
|
1.0
|
CB
|
A:CAS89
|
3.1
|
47.9
|
1.0
|
CA
|
A:CAS89
|
3.7
|
42.8
|
1.0
|
N
|
A:ILE90
|
4.1
|
38.0
|
1.0
|
C
|
A:CAS89
|
4.2
|
38.3
|
1.0
|
O
|
A:HOH256
|
4.4
|
40.8
|
1.0
|
OE2
|
A:GLU91
|
4.6
|
61.3
|
1.0
|
O
|
A:ILE90
|
4.7
|
36.2
|
1.0
|
C
|
A:ILE90
|
4.8
|
36.9
|
1.0
|
|
Arsenic binding site 3 out
of 12 in 4w9c
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Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:As77
b:55.3
occ:1.00
|
AS
|
C:CAS77
|
0.0
|
55.3
|
1.0
|
CE1
|
C:CAS77
|
2.0
|
56.5
|
1.0
|
CE2
|
C:CAS77
|
2.0
|
58.5
|
1.0
|
SG
|
C:CAS77
|
2.2
|
43.3
|
1.0
|
CB
|
C:CAS77
|
3.1
|
37.4
|
1.0
|
CA
|
C:CAS77
|
3.6
|
33.2
|
1.0
|
CE
|
K:MET45
|
3.8
|
68.4
|
1.0
|
CA
|
C:GLY106
|
4.3
|
39.7
|
1.0
|
O
|
C:THR105
|
4.4
|
40.6
|
1.0
|
C
|
C:CAS77
|
4.4
|
33.0
|
1.0
|
CZ
|
C:PHE148
|
4.5
|
63.4
|
1.0
|
N
|
C:GLY106
|
4.6
|
39.8
|
1.0
|
C
|
C:THR105
|
4.6
|
40.6
|
1.0
|
N
|
C:ASN78
|
4.6
|
32.0
|
1.0
|
CG
|
K:MET45
|
4.8
|
61.8
|
1.0
|
CE2
|
C:PHE148
|
4.9
|
63.6
|
1.0
|
N
|
C:CAS77
|
4.9
|
31.5
|
1.0
|
SD
|
K:MET45
|
4.9
|
66.8
|
1.0
|
O
|
C:PHE76
|
5.0
|
30.9
|
1.0
|
NH2
|
C:ARG79
|
5.0
|
69.3
|
1.0
|
|
Arsenic binding site 4 out
of 12 in 4w9c
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Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As60
b:47.1
occ:1.00
|
AS
|
D:CAS60
|
0.0
|
47.1
|
1.0
|
CE1
|
D:CAS60
|
2.0
|
49.6
|
1.0
|
CE2
|
D:CAS60
|
2.0
|
52.6
|
1.0
|
SG
|
D:CAS60
|
2.2
|
40.8
|
1.0
|
CB
|
D:CAS60
|
3.2
|
34.0
|
1.0
|
CA
|
D:CAS60
|
3.4
|
31.4
|
1.0
|
N
|
D:CAS60
|
4.0
|
30.6
|
1.0
|
CD2
|
D:LEU51
|
4.3
|
42.8
|
1.0
|
NE2
|
D:GLN49
|
4.3
|
37.3
|
1.0
|
O
|
D:GLU59
|
4.4
|
30.9
|
1.0
|
C
|
D:GLU59
|
4.4
|
30.8
|
1.0
|
C
|
D:CAS60
|
4.6
|
29.0
|
1.0
|
CG
|
D:LYS55
|
4.7
|
41.7
|
1.0
|
CB
|
D:LYS55
|
4.8
|
40.4
|
1.0
|
CD
|
D:GLN49
|
4.9
|
36.7
|
1.0
|
O
|
D:CAS60
|
4.9
|
28.9
|
1.0
|
|
Arsenic binding site 5 out
of 12 in 4w9c
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Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:As89
b:0.6
occ:1.00
|
AS
|
D:CAS89
|
0.0
|
0.6
|
1.0
|
CE1
|
D:CAS89
|
2.0
|
0.0
|
1.0
|
CE2
|
D:CAS89
|
2.0
|
0.5
|
1.0
|
SG
|
D:CAS89
|
2.2
|
94.0
|
1.0
|
CB
|
D:CAS89
|
3.1
|
81.1
|
1.0
|
CA
|
D:CAS89
|
3.7
|
72.4
|
1.0
|
N
|
D:ILE90
|
4.3
|
62.1
|
1.0
|
C
|
D:CAS89
|
4.3
|
66.0
|
1.0
|
O
|
D:HOH224
|
4.7
|
61.2
|
1.0
|
OE1
|
D:GLU91
|
4.9
|
82.5
|
1.0
|
C
|
D:ILE90
|
4.9
|
57.0
|
1.0
|
|
Arsenic binding site 6 out
of 12 in 4w9c
Go back to
Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (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 (2S,4R)-1-(3,3-Dimethylbutanoyl)-4- Hydroxy-N-(4-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:As77
b:55.2
occ:1.00
|
AS
|
F:CAS77
|
0.0
|
55.2
|
1.0
|
CE1
|
F:CAS77
|
2.0
|
54.1
|
1.0
|
CE2
|
F:CAS77
|
2.0
|
56.8
|
1.0
|
SG
|
F:CAS77
|
2.2
|
45.0
|
1.0
|
CB
|
F:CAS77
|
3.1
|
39.0
|
1.0
|
CA
|
F:CAS77
|
3.7
|
35.1
|
1.0
|
CE
|
H:MET45
|
4.1
|
75.3
|
1.0
|
CA
|
F:GLY106
|
4.2
|
40.8
|
1.0
|
O
|
F:THR105
|
4.3
|
35.5
|
1.0
|
N
|
F:GLY106
|
4.4
|
39.5
|
1.0
|
C
|
F:CAS77
|
4.4
|
33.2
|
1.0
|
C
|
F:THR105
|
4.4
|
38.8
|
1.0
|
CZ
|
F:PHE148
|
4.5
|
56.5
|
1.0
|
N
|
F:ASN78
|
4.6
|
32.1
|
1.0
|
CG
|
H:MET45
|
4.8
|
68.0
|
1.0
|
CE2
|
F:PHE148
|
4.8
|
54.9
|
1.0
|
SD
|
H:MET45
|
4.9
|
74.7
|
1.0
|
N
|
F:CAS77
|
4.9
|
33.7
|
1.0
|
O
|
F:PHE76
|
5.0
|
32.9
|
1.0
|
|
Arsenic binding site 7 out
of 12 in 4w9c
Go back to
Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As60
b:51.5
occ:1.00
|
AS
|
G:CAS60
|
0.0
|
51.5
|
1.0
|
CE2
|
G:CAS60
|
2.0
|
52.5
|
1.0
|
CE1
|
G:CAS60
|
2.0
|
52.5
|
1.0
|
SG
|
G:CAS60
|
2.2
|
49.0
|
1.0
|
CB
|
G:CAS60
|
3.1
|
42.9
|
1.0
|
CA
|
G:CAS60
|
3.3
|
41.3
|
1.0
|
CD2
|
G:LEU51
|
3.9
|
37.5
|
1.0
|
N
|
G:CAS60
|
4.0
|
40.3
|
1.0
|
NE2
|
G:GLN49
|
4.2
|
36.1
|
1.0
|
C
|
G:CAS60
|
4.5
|
40.1
|
1.0
|
C
|
G:GLU59
|
4.6
|
41.4
|
1.0
|
O
|
G:GLU59
|
4.6
|
41.1
|
1.0
|
CD
|
G:GLN49
|
4.6
|
34.9
|
1.0
|
CB
|
G:LYS55
|
4.6
|
45.2
|
1.0
|
CG
|
G:LYS55
|
4.6
|
47.6
|
1.0
|
O
|
G:CAS60
|
4.8
|
40.4
|
1.0
|
OE1
|
G:GLN49
|
4.8
|
34.2
|
1.0
|
|
Arsenic binding site 8 out
of 12 in 4w9c
Go back to
Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:As89
b:66.3
occ:1.00
|
AS
|
G:CAS89
|
0.0
|
66.3
|
1.0
|
CE1
|
G:CAS89
|
2.0
|
64.7
|
1.0
|
CE2
|
G:CAS89
|
2.0
|
71.3
|
1.0
|
SG
|
G:CAS89
|
2.2
|
51.1
|
1.0
|
CB
|
G:CAS89
|
3.0
|
41.2
|
1.0
|
O
|
G:HOH240
|
3.3
|
46.8
|
1.0
|
CA
|
G:CAS89
|
3.5
|
36.9
|
1.0
|
O
|
G:HOH236
|
3.8
|
44.2
|
1.0
|
O
|
G:HOH224
|
3.8
|
43.1
|
1.0
|
N
|
G:ILE90
|
4.0
|
33.2
|
1.0
|
C
|
G:CAS89
|
4.1
|
33.3
|
1.0
|
O
|
G:ILE90
|
4.6
|
32.5
|
1.0
|
C
|
G:ILE90
|
4.8
|
32.8
|
1.0
|
N
|
G:CAS89
|
4.9
|
37.0
|
1.0
|
O
|
G:LEU88
|
5.0
|
40.9
|
1.0
|
|
Arsenic binding site 9 out
of 12 in 4w9c
Go back to
Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:As77
b:44.3
occ:1.00
|
AS
|
I:CAS77
|
0.0
|
44.3
|
1.0
|
CE1
|
I:CAS77
|
2.0
|
46.5
|
1.0
|
CE2
|
I:CAS77
|
2.0
|
44.9
|
1.0
|
SG
|
I:CAS77
|
2.2
|
38.6
|
1.0
|
CB
|
I:CAS77
|
3.1
|
32.4
|
1.0
|
CA
|
I:CAS77
|
3.5
|
28.9
|
1.0
|
CA
|
I:GLY106
|
3.9
|
33.1
|
1.0
|
O
|
I:THR105
|
4.1
|
32.5
|
1.0
|
C
|
I:CAS77
|
4.2
|
27.9
|
1.0
|
N
|
I:GLY106
|
4.2
|
32.9
|
1.0
|
C
|
I:THR105
|
4.3
|
33.4
|
1.0
|
N
|
I:ASN78
|
4.3
|
27.5
|
1.0
|
N
|
I:CAS77
|
4.8
|
26.9
|
1.0
|
CE2
|
I:PHE148
|
4.9
|
40.0
|
1.0
|
O
|
I:PHE76
|
5.0
|
28.2
|
1.0
|
|
Arsenic binding site 10 out
of 12 in 4w9c
Go back to
Arsenic Binding Sites List in 4w9c
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2)
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-(Oxazol-5-Yl)Benzyl)Pyrrolidine-2-Carboxamide (Ligand 2) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:As60
b:49.5
occ:1.00
|
AS
|
J:CAS60
|
0.0
|
49.5
|
1.0
|
CE2
|
J:CAS60
|
2.0
|
53.7
|
1.0
|
CE1
|
J:CAS60
|
2.0
|
52.7
|
1.0
|
SG
|
J:CAS60
|
2.3
|
40.9
|
1.0
|
CB
|
J:CAS60
|
3.3
|
33.0
|
1.0
|
CA
|
J:CAS60
|
3.5
|
30.5
|
1.0
|
CD2
|
J:LEU51
|
3.9
|
30.0
|
1.0
|
N
|
J:CAS60
|
4.1
|
28.9
|
1.0
|
O
|
J:GLU59
|
4.4
|
29.7
|
1.0
|
NE2
|
J:GLN49
|
4.5
|
35.3
|
1.0
|
C
|
J:GLU59
|
4.6
|
30.0
|
1.0
|
CG
|
J:LYS55
|
4.6
|
32.7
|
1.0
|
CB
|
J:LYS55
|
4.7
|
30.4
|
1.0
|
C
|
J:CAS60
|
4.7
|
29.8
|
1.0
|
CD
|
J:GLN49
|
4.9
|
33.4
|
1.0
|
O
|
J:CAS60
|
4.9
|
30.1
|
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 12:29:34 2024
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