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Arsenic in PDB 4b9k: Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound

Protein crystallography data

The structure of Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound, PDB code: 4b9k was solved by D.L.Buckley, J.L.Gustafson, I.Vanmolle, A.G.Roth, H.Seoptae, P.C.Gareiss, W.L.Jorgensen, A.Ciulli, C.M.Crews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.06 / 2.00
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 92.860, 92.860, 364.390, 90.00, 90.00, 90.00
R / Rfree (%) 18.88 / 22.03

Arsenic Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Arsenic atom in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound (pdb code 4b9k). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 15 binding sites of Arsenic where determined in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound, PDB code: 4b9k:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Arsenic binding site 1 out of 15 in 4b9k

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Arsenic binding site 1 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:42.0
occ:0.44
 AS A:CAS60 0.0 42.0 0.4
CE1 A:CAS60 2.0 42.7 0.4
CE2 A:CAS60 2.0 41.2 0.4
SG A:CAS60 2.4 38.3 1.0
CB A:CAS60 3.4 34.6 1.0
CA A:CAS60 3.5 32.6 1.0
CD2 A:LEU51 3.7 35.9 1.0
N A:CAS60 4.2 31.0 1.0
NE2 A:GLN49 4.4 33.1 1.0
O A:GLU59 4.4 33.0 1.0
CB A:LYS55 4.5 29.5 1.0
CG A:LYS55 4.5 35.4 1.0
C A:GLU59 4.6 33.2 1.0
C A:CAS60 4.6 36.2 1.0
CA A:LEU51 4.8 32.6 1.0
O A:CAS60 4.8 34.5 1.0
CG A:LEU51 4.9 33.0 1.0
CB A:LEU51 4.9 30.1 1.0
N A:ASP52 4.9 35.2 1.0
CD A:GLN49 4.9 45.6 1.0

Arsenic binding site 2 out of 15 in 4b9k

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Arsenic binding site 2 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:62.9
occ:0.58
 AS A:CAS89 0.0 62.9 0.6
SG A:CAS89 1.6 57.6 0.4
CE1 A:CAS89 2.0 60.8 0.6
CE2 A:CAS89 2.0 64.0 0.6
SG A:CAS89 2.3 58.5 0.6
AS A:CAS89 3.0 60.1 0.4
CE1 A:CAS89 3.2 60.8 0.4
CB A:CAS89 3.2 53.1 0.6
CB A:CAS89 3.3 52.3 0.4
CA A:CAS89 3.7 46.4 0.6
CA A:CAS89 3.7 46.5 0.4
O A:HOH2086 4.0 47.4 1.0
N A:ILE90 4.2 41.4 1.0
C A:CAS89 4.2 45.5 0.6
C A:CAS89 4.2 45.9 0.4
CE2 A:CAS89 4.4 62.3 0.4
O A:ILE90 4.6 43.7 1.0
C A:ILE90 4.9 43.5 1.0
O A:LEU88 4.9 48.3 1.0
N A:CAS89 5.0 45.2 0.6
N A:CAS89 5.0 45.3 0.4

Arsenic binding site 3 out of 15 in 4b9k

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Arsenic binding site 3 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:60.1
occ:0.42
 AS A:CAS89 0.0 60.1 0.4
SG A:CAS89 1.5 58.5 0.6
CE2 A:CAS89 2.0 62.3 0.4
CE1 A:CAS89 2.0 60.8 0.4
SG A:CAS89 2.3 57.6 0.4
AS A:CAS89 3.0 62.9 0.6
CB A:CAS89 3.1 52.3 0.4
CB A:CAS89 3.2 53.1 0.6
CE1 A:CAS89 3.7 60.8 0.6
CG A:GLU91 3.8 58.6 1.0
C A:CAS89 3.8 45.5 0.6
C A:CAS89 3.8 45.9 0.4
CA A:CAS89 4.0 46.5 0.4
CA A:CAS89 4.0 46.4 0.6
O A:CAS89 4.0 43.4 0.6
O A:CAS89 4.0 44.2 0.4
N A:ILE90 4.1 41.4 1.0
N A:GLU91 4.1 39.9 1.0
CA A:HIS10 4.2 35.5 1.0
ND1 A:HIS10 4.2 45.0 1.0
CG A:HIS10 4.3 43.4 1.0
C A:ILE90 4.4 43.5 1.0
CE1 A:HIS10 4.5 46.4 1.0
CA A:GLU91 4.6 39.2 1.0
CB A:HIS10 4.7 37.6 1.0
CA A:ILE90 4.7 38.6 1.0
CD2 A:HIS10 4.7 47.5 1.0
CB A:GLU91 4.7 41.2 1.0
CE2 A:CAS89 4.7 64.0 0.6
NE2 A:HIS10 4.8 48.4 1.0
O A:ILE90 4.8 43.7 1.0
N A:HIS10 5.0 35.0 1.0

Arsenic binding site 4 out of 15 in 4b9k

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Arsenic binding site 4 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:51.2
occ:0.62
 AS C:CAS77 0.0 51.2 0.6
CE2 C:CAS77 2.0 54.4 0.6
CE1 C:CAS77 2.0 51.3 0.6
SG C:CAS77 2.2 46.6 1.0
CB C:CAS77 3.1 40.0 1.0
CA C:CAS77 3.6 36.0 1.0
CA C:GLY106 4.0 48.2 1.0
O C:THR105 4.3 46.7 1.0
CZ C:PHE148 4.3 56.0 1.0
N C:GLY106 4.3 48.2 1.0
C C:CAS77 4.4 38.7 1.0
C C:THR105 4.5 50.3 1.0
SD K:MET45 4.5 54.4 1.0
CE1 C:PHE148 4.6 55.8 1.0
N C:ASN78 4.7 34.2 1.0
CG K:MET45 4.7 50.0 1.0
N C:CAS77 4.9 33.2 1.0

Arsenic binding site 5 out of 15 in 4b9k

Go back to Arsenic Binding Sites List in 4b9k
Arsenic binding site 5 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:49.3
occ:0.53
 AS D:CAS60 0.0 49.3 0.5
CE1 D:CAS60 2.0 50.7 0.5
CE2 D:CAS60 2.0 48.9 0.5
SG D:CAS60 2.3 48.0 1.0
CB D:CAS60 3.3 41.6 1.0
CA D:CAS60 3.5 37.5 1.0
CD2 D:LEU51 3.8 45.7 1.0
N D:CAS60 4.2 36.7 1.0
NE2 D:GLN49 4.3 37.8 1.0
O D:GLU59 4.6 37.3 1.0
CB D:LYS55 4.6 46.6 1.0
CG D:LYS55 4.6 58.7 1.0
O D:HOH2036 4.7 49.0 1.0
C D:GLU59 4.7 38.2 1.0
C D:CAS60 4.7 38.9 1.0
CD D:GLN49 4.8 45.4 1.0
O D:CAS60 4.9 37.8 1.0
CA D:LEU51 4.9 44.0 1.0

Arsenic binding site 6 out of 15 in 4b9k

Go back to Arsenic Binding Sites List in 4b9k
Arsenic binding site 6 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:76.3
occ:0.50
 AS D:CAS89 0.0 76.3 0.5
SG D:CAS89 1.6 71.7 0.5
CE2 D:CAS89 2.0 76.5 0.5
CE1 D:CAS89 2.0 72.7 0.5
SG D:CAS89 2.2 72.8 0.5
AS D:CAS89 3.0 74.2 0.5
CB D:CAS89 3.2 68.8 0.5
CE1 D:CAS89 3.2 74.9 0.5
CB D:CAS89 3.3 67.9 0.5
CA D:CAS89 3.7 61.8 0.5
CA D:CAS89 3.7 61.4 0.5
N D:ILE90 4.2 56.9 1.0
C D:CAS89 4.3 62.2 0.5
C D:CAS89 4.3 62.1 0.5
O D:HOH2054 4.3 49.8 1.0
CE2 D:CAS89 4.4 78.4 0.5
O D:HOH2055 4.4 57.7 1.0
O D:ILE90 4.7 58.7 1.0
O D:LEU88 4.9 61.2 1.0
C D:ILE90 4.9 58.4 1.0
N D:CAS89 5.0 60.7 0.5
N D:CAS89 5.0 60.4 0.5

Arsenic binding site 7 out of 15 in 4b9k

Go back to Arsenic Binding Sites List in 4b9k
Arsenic binding site 7 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:74.2
occ:0.49
 AS D:CAS89 0.0 74.2 0.5
SG D:CAS89 1.6 72.8 0.5
CE1 D:CAS89 2.0 74.9 0.5
CE2 D:CAS89 2.0 78.4 0.5
SG D:CAS89 2.3 71.7 0.5
AS D:CAS89 3.0 76.3 0.5
CB D:CAS89 3.2 67.9 0.5
CB D:CAS89 3.3 68.8 0.5
CE1 D:CAS89 3.6 72.7 0.5
C D:CAS89 3.8 62.2 0.5
C D:CAS89 3.8 62.1 0.5
ND1 D:HIS10 4.0 64.0 1.0
CA D:CAS89 4.0 61.4 0.5
CA D:CAS89 4.0 61.8 0.5
O D:CAS89 4.1 61.1 0.5
O D:CAS89 4.1 61.0 0.5
N D:ILE90 4.1 56.9 1.0
N D:GLU91 4.1 55.3 1.0
CA D:HIS10 4.2 52.4 1.0
CG D:HIS10 4.3 62.7 1.0
CE1 D:HIS10 4.3 65.8 1.0
C D:ILE90 4.4 58.4 1.0
CA D:GLU91 4.5 56.0 1.0
CB D:HIS10 4.6 56.5 1.0
CB D:GLU91 4.6 59.1 1.0
CA D:ILE90 4.7 53.9 1.0
CE2 D:CAS89 4.7 76.5 0.5
CD2 D:HIS10 4.8 67.3 1.0
O D:ILE90 4.8 58.7 1.0
OE1 D:GLU91 4.8 0.5 1.0
NE2 D:HIS10 4.9 68.8 1.0
O D:HOH2055 4.9 57.7 1.0
N D:HIS10 5.0 50.7 1.0
C D:HIS10 5.0 52.8 1.0

Arsenic binding site 8 out of 15 in 4b9k

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Arsenic binding site 8 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:As112

b:57.4
occ:0.28
 AS E:CAS112 0.0 57.4 0.3
CE1 E:CAS112 2.0 58.7 0.3
CE2 E:CAS112 2.0 58.1 0.3
SG E:CAS112 2.2 55.1 1.0
CB E:CAS112 2.7 54.1 1.0
CE1 E:PHE77 3.1 45.9 1.0
CZ E:PHE77 3.8 45.2 1.0
CB E:SER39 3.9 47.8 1.0
CD1 E:PHE77 4.0 43.6 1.0
CA E:CAS112 4.2 53.0 1.0
CG1 E:VAL73 4.2 32.2 1.0
CB E:LEU110 4.3 33.9 1.0
OG E:SER39 4.6 50.4 1.0
CD1 E:LEU110 4.6 36.8 1.0
CG2 E:THR38 4.7 57.5 1.0
N E:CAS112 4.8 45.6 1.0
CA E:SER39 4.8 45.4 1.0
CD2 E:TYR76 4.8 28.0 1.0
C E:CAS112 4.9 57.9 1.0
O E:LEU110 5.0 41.6 1.0

Arsenic binding site 9 out of 15 in 4b9k

Go back to Arsenic Binding Sites List in 4b9k
Arsenic binding site 9 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:45.6
occ:0.64
 AS F:CAS77 0.0 45.6 0.6
CE1 F:CAS77 2.0 47.5 0.6
CE2 F:CAS77 2.0 46.0 0.6
SG F:CAS77 2.2 40.9 1.0
CB F:CAS77 3.1 34.5 1.0
CA F:CAS77 3.6 30.4 1.0
CA F:GLY106 4.0 36.7 1.0
N F:GLY106 4.2 37.5 1.0
O F:THR105 4.2 39.3 1.0
CE H:MET45 4.3 41.1 1.0
C F:THR105 4.3 41.8 1.0
C F:CAS77 4.3 32.1 1.0
CZ F:PHE148 4.4 44.0 1.0
N F:ASN78 4.6 28.6 1.0
CG H:MET45 4.8 43.2 1.0
CH3 H:ACT1113 4.8 61.1 1.0
CE1 F:PHE148 4.8 44.1 1.0
N F:CAS77 4.9 29.5 1.0

Arsenic binding site 10 out of 15 in 4b9k

Go back to Arsenic Binding Sites List in 4b9k
Arsenic binding site 10 out of 15 in the Pvhl-Elob-Eloc COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound


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 COMPLEX_(2S,4R)-1-(3-Amino-2-Methylbenzoyl)-4- Hydroxy-N-(4-(4-Methylthiazol-5-Yl)Benzyl) Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
G:As60

b:47.9
occ:0.62
 AS G:CAS60 0.0 47.9 0.6
CE2 G:CAS60 2.0 49.4 0.6
CE1 G:CAS60 2.0 47.6 0.6
SG G:CAS60 2.3 47.0 1.0
CB G:CAS60 3.3 41.1 1.0
CA G:CAS60 3.4 38.9 1.0
CD2 G:LEU51 3.7 38.4 1.0
N G:CAS60 4.2 39.5 1.0
NE2 G:GLN49 4.2 37.3 1.0
O G:GLU59 4.5 44.5 1.0
C G:CAS60 4.6 40.5 1.0
CB G:LYS55 4.6 43.3 1.0
C G:GLU59 4.7 44.5 1.0
CG G:LYS55 4.7 49.7 1.0
CD G:GLN49 4.7 41.5 1.0
O G:CAS60 4.8 38.5 1.0
CA G:LEU51 5.0 34.6 1.0

Reference:

D.L.Buckley, J.L.Gustafson, I.Van Molle, A.G.Roth, H.S.Tae, P.C.Gareiss, W.L.Jorgensen, A.Ciulli, C.M.Crews. Small-Molecule Inhibitors of the Interaction Between the E3 Ligase Vhl and HIF1 Alpha Angew.Chem.Int.Ed.Engl. V. 51 11463 2012.
ISSN: ISSN 1433-7851
PubMed: 23065727
DOI: 10.1002/ANIE.201206231
Page generated: Wed Jul 10 11:57:31 2024

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