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Arsenic in PDB 8bdm: Vcb in Complex with Compound 26

Protein crystallography data

The structure of Vcb in Complex with Compound 26, PDB code: 8bdm was solved by F.J.Sorrell, J.E.Mueller, M.Lehmann, A.Wegener, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.74 / 2.02
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.894, 92.894, 364.016, 90, 90, 90
R / Rfree (%) 22.5 / 25.5

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Vcb in Complex with Compound 26 (pdb code 8bdm). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 8 binding sites of Arsenic where determined in the Vcb in Complex with Compound 26, PDB code: 8bdm:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Arsenic binding site 1 out of 8 in 8bdm

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Arsenic binding site 1 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As89

b:124.5
occ:1.00
 AS G:CAS89 0.0 124.5 1.0
CE1 G:CAS89 2.0 124.7 1.0
CE2 G:CAS89 2.0 124.5 1.0
SG G:CAS89 2.2 120.7 1.0
CB G:CAS89 3.2 102.9 1.0
OE2 G:GLU91 3.7 109.1 1.0
CG G:GLU91 3.8 97.4 1.0
C G:CAS89 4.0 94.6 1.0
CA G:CAS89 4.1 97.9 1.0
N G:ILE90 4.1 92.0 1.0
CD G:GLU91 4.1 106.3 1.0
N G:GLU91 4.2 86.8 1.0
C G:ILE90 4.3 87.9 1.0
CA G:GLU91 4.5 86.5 1.0
O G:CAS89 4.5 94.3 1.0
O G:ILE90 4.6 87.7 1.0
CA G:ILE90 4.7 89.9 1.0
CB G:GLU91 4.7 90.0 1.0
CA G:HIS10 4.9 71.2 1.0

Arsenic binding site 2 out of 8 in 8bdm

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Arsenic binding site 2 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:As77

b:78.2
occ:1.00
 AS I:CAS77 0.0 78.2 1.0
CE1 I:CAS77 2.0 78.4 1.0
CE2 I:CAS77 2.0 78.4 1.0
SG I:CAS77 2.3 75.5 1.0
CB I:CAS77 3.3 60.5 1.0
CA I:CAS77 3.5 56.1 1.0
CA I:GLY106 3.9 58.3 1.0
CE B:MET45 3.9 99.4 1.0
N I:GLY106 4.1 57.1 1.0
O I:THR105 4.1 56.2 1.0
C I:CAS77 4.1 53.8 1.0
C I:THR105 4.2 56.8 1.0
N I:ASN78 4.3 53.0 1.0
CE2 I:PHE148 4.6 70.4 1.0
N I:CAS77 4.8 55.2 1.0
O I:PHE76 4.9 55.3 1.0
O I:GLY104 4.9 58.2 1.0
CZ B:PHE109 4.9 66.1 1.0
O I:CAS77 4.9 53.3 1.0

Arsenic binding site 3 out of 8 in 8bdm

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Arsenic binding site 3 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:99.5
occ:1.00
 AS D:CAS89 0.0 99.5 1.0
CE1 D:CAS89 2.0 99.4 1.0
CE2 D:CAS89 2.0 99.6 1.0
SG D:CAS89 2.3 96.0 1.0
CB D:CAS89 2.9 72.8 1.0
CA D:CAS89 3.3 66.4 1.0
C D:CAS89 3.8 62.9 1.0
N D:ILE90 3.8 60.6 1.0
O D:HOH262 4.3 64.8 1.0
N D:CAS89 4.6 65.1 1.0
O D:CAS89 4.6 62.6 1.0
O D:ILE90 4.7 58.4 1.0
C D:ILE90 4.7 58.4 1.0
OE1 D:GLU91 4.7 85.9 1.0
O D:HOH278 4.9 68.1 1.0
CA D:ILE90 4.9 59.2 1.0
O D:LEU88 4.9 64.6 1.0

Arsenic binding site 4 out of 8 in 8bdm

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Arsenic binding site 4 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:80.3
occ:1.00
 AS F:CAS77 0.0 80.3 1.0
CE2 F:CAS77 2.0 80.7 1.0
CE1 F:CAS77 2.0 80.0 1.0
SG F:CAS77 2.3 76.6 1.0
CB F:CAS77 3.2 61.0 1.0
CA F:CAS77 3.7 56.5 1.0
CA F:GLY106 4.0 60.1 1.0
N F:GLY106 4.2 59.5 1.0
O F:THR105 4.3 59.5 1.0
C F:THR105 4.4 59.7 1.0
C F:CAS77 4.4 55.6 1.0
CE2 F:PHE148 4.4 66.1 1.0
N F:ASN78 4.5 54.6 1.0
O F:HOH402 4.7 61.4 1.0
CZ F:PHE148 4.7 66.1 1.0
N F:CAS77 4.9 54.4 1.0
O F:PHE76 5.0 53.4 1.0

Arsenic binding site 5 out of 8 in 8bdm

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Arsenic binding site 5 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:95.1
occ:1.00
 AS A:CAS89 0.0 95.1 1.0
CE2 A:CAS89 2.0 95.3 1.0
CE1 A:CAS89 2.0 95.1 1.0
SG A:CAS89 2.2 90.9 1.0
CB A:CAS89 3.2 71.9 1.0
OE2 A:GLU91 3.9 73.1 1.0
CG A:GLU91 3.9 64.2 1.0
C A:CAS89 4.0 63.4 1.0
CA A:CAS89 4.0 66.6 1.0
N A:ILE90 4.1 61.5 1.0
CD A:GLU91 4.2 70.3 1.0
N A:GLU91 4.2 57.5 1.0
C A:ILE90 4.3 59.0 1.0
O A:CAS89 4.4 62.5 1.0
CA A:GLU91 4.5 56.8 1.0
O A:ILE90 4.6 59.1 1.0
CA A:ILE90 4.7 59.8 1.0
CB A:GLU91 4.8 59.0 1.0
CA A:HIS10 4.8 52.6 1.0
CG A:HIS10 4.9 55.5 1.0
CD2 A:HIS10 5.0 57.1 1.0

Arsenic binding site 6 out of 8 in 8bdm

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Arsenic binding site 6 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:71.2
occ:1.00
 AS C:CAS77 0.0 71.2 1.0
CE2 C:CAS77 2.0 70.7 1.0
CE1 C:CAS77 2.0 70.8 1.0
SG C:CAS77 2.3 67.4 1.0
CB C:CAS77 3.3 54.0 1.0
CA C:CAS77 3.5 49.8 1.0
CA C:GLY106 3.8 52.4 1.0
N C:GLY106 4.0 53.2 1.0
O C:THR105 4.1 54.1 1.0
C C:CAS77 4.2 48.1 1.0
C C:THR105 4.2 54.3 1.0
N C:ASN78 4.3 48.3 1.0
CE2 C:PHE148 4.7 56.8 1.0
N C:CAS77 4.8 48.2 1.0
O C:PHE76 4.9 47.0 1.0
O C:GLY104 5.0 56.9 1.0
O C:CAS77 5.0 47.4 1.0

Arsenic binding site 7 out of 8 in 8bdm

Go back to Arsenic Binding Sites List in 8bdm
Arsenic binding site 7 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 7 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:As89

b:92.8
occ:1.00
 AS J:CAS89 0.0 92.8 1.0
CE2 J:CAS89 2.0 92.9 1.0
CE1 J:CAS89 2.1 92.6 1.0
SG J:CAS89 2.3 88.1 1.0
CB J:CAS89 3.0 64.8 1.0
CA J:CAS89 3.6 58.5 1.0
O J:HOH254 3.9 54.3 1.0
N J:ILE90 3.9 53.7 1.0
C J:CAS89 4.0 55.4 1.0
O J:HOH284 4.4 68.8 1.0
O J:ILE90 4.5 52.5 1.0
C J:ILE90 4.6 52.2 1.0
O J:HOH282 4.8 57.8 1.0
O J:HOH257 4.8 55.1 1.0
O J:CAS89 4.9 54.9 1.0
OE2 J:GLU91 4.9 68.5 1.0
CA J:ILE90 4.9 52.7 1.0
N J:CAS89 4.9 56.5 1.0

Arsenic binding site 8 out of 8 in 8bdm

Go back to Arsenic Binding Sites List in 8bdm
Arsenic binding site 8 out of 8 in the Vcb in Complex with Compound 26


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 8 of Vcb in Complex with Compound 26 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:As77

b:61.1
occ:1.00
 AS L:CAS77 0.0 61.1 1.0
CE1 L:CAS77 2.0 61.3 1.0
CE2 L:CAS77 2.0 60.8 1.0
SG L:CAS77 2.2 56.0 1.0
CB L:CAS77 3.3 43.7 1.0
CA L:CAS77 3.5 41.0 1.0
CA L:GLY106 3.8 42.8 1.0
N L:GLY106 4.0 42.6 1.0
O L:THR105 4.1 42.7 1.0
C L:CAS77 4.1 40.4 1.0
C L:THR105 4.2 43.0 1.0
N L:ASN78 4.3 40.2 1.0
CE2 L:PHE148 4.7 51.4 1.0
N L:CAS77 4.8 40.5 1.0
O L:PHE76 4.9 39.4 1.0
O L:GLY104 4.9 47.3 1.0
O L:CAS77 5.0 40.1 1.0

Reference:

J.Krieger, F.J.Sorell, A.A.Wegener, B.Leuthner, F.Machrouhi-Porcher, M.Hecht, E.M.Leibrock, J.E.Mueller, J.Eisert, I.V.Hartung, S.Schlesiger. Systematic Potency & Property Assessment of Vhl Ligands and Implications on Protac Design. Chemmedchem 2023.
ISSN: ESSN 1860-7187
PubMed: 36749883
DOI: 10.1002/CMDC.202200615
Page generated: Mon Jul 7 01:06:07 2025

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