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Chlorine in PDB 4b95: Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound

Protein crystallography data

The structure of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound, PDB code: 4b95 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) 27.59 / 2.80
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 93.040, 93.040, 362.430, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound (pdb code 4b95). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound, PDB code: 4b95:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4b95

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Chlorine binding site 1 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1206

b:65.8
occ:1.00
 CL1 C:UCK1206 0.0 65.8 1.0
C11 C:UCK1206 1.8 63.5 1.0
C13 C:UCK1206 2.7 62.0 1.0
NH1 C:ARG107 2.8 86.8 1.0
C10 C:UCK1206 2.8 61.4 1.0
CD C:PRO99 3.4 43.3 1.0
O C:PRO99 3.7 46.8 1.0
CZ C:ARG107 3.8 97.3 1.0
CD C:ARG107 3.8 75.3 1.0
CB C:TYR98 4.0 45.2 1.0
N C:PRO99 4.0 42.0 1.0
C14 C:UCK1206 4.0 60.9 1.0
C09 C:UCK1206 4.1 61.2 1.0
NE C:ARG107 4.2 85.9 1.0
CG2 C:ILE109 4.2 56.4 1.0
CG C:PRO99 4.2 48.9 1.0
CD2 C:TYR98 4.3 50.1 1.0
CB C:PRO99 4.4 45.4 1.0
C C:PRO99 4.5 46.7 1.0
CA C:PRO99 4.6 42.6 1.0
CG C:TYR98 4.6 48.2 1.0
C08 C:UCK1206 4.6 60.9 1.0
CG C:PRO86 4.6 43.8 1.0
C C:TYR98 4.6 45.7 1.0
NH2 C:ARG107 4.8 76.5 1.0
CE2 C:PHE76 4.9 35.8 1.0
CA C:TYR98 4.9 44.2 1.0
CD2 C:PHE76 4.9 34.5 1.0

Chlorine binding site 2 out of 8 in 4b95

Go back to Chlorine Binding Sites List in 4b95
Chlorine binding site 2 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1206

b:63.4
occ:1.00
 CL2 C:UCK1206 0.0 63.4 1.0
C19 C:UCK1206 1.7 59.3 1.0
C21 C:UCK1206 2.7 54.8 1.0
C18 C:UCK1206 2.8 59.7 1.0
C17 C:UCK1206 3.1 60.7 1.0
OH C:TYR98 3.2 59.5 1.0
N16 C:UCK1206 3.3 58.8 1.0
C26 C:UCK1206 3.5 57.2 1.0
O15 C:UCK1206 3.7 59.6 1.0
OE1 C:GLN96 3.8 59.2 1.0
O25 C:UCK1206 3.8 62.6 1.0
C22 C:UCK1206 4.0 54.3 1.0
CZ3 C:TRP88 4.0 43.7 1.0
C24 C:UCK1206 4.0 58.6 1.0
O C:HOH2021 4.4 33.8 1.0
C04 C:UCK1206 4.4 59.0 1.0
C05 C:UCK1206 4.5 60.3 1.0
C23 C:UCK1206 4.5 56.4 1.0
CE3 C:TRP88 4.5 41.2 1.0
CH2 C:TRP88 4.6 45.0 1.0
CZ C:TYR98 4.6 58.0 1.0
CD C:GLN96 4.9 78.0 1.0
C02 C:UCK1206 5.0 54.6 1.0

Chlorine binding site 3 out of 8 in 4b95

Go back to Chlorine Binding Sites List in 4b95
Chlorine binding site 3 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1206

b:92.9
occ:1.00
 CL1 F:UCK1206 0.0 92.9 1.0
C11 F:UCK1206 1.8 91.3 1.0
C13 F:UCK1206 2.8 89.0 1.0
C10 F:UCK1206 2.8 90.4 1.0
NE F:ARG107 3.4 82.2 1.0
O F:PRO99 3.4 53.3 1.0
CD F:PRO99 3.4 49.9 1.0
CD F:ARG107 3.6 62.3 1.0
N F:PRO99 3.9 47.8 1.0
CZ F:ARG107 3.9 0.6 1.0
CG F:PRO99 4.0 56.2 1.0
C14 F:UCK1206 4.0 87.3 1.0
C09 F:UCK1206 4.1 89.5 1.0
CB F:PRO99 4.1 51.6 1.0
CB F:TYR98 4.2 48.5 1.0
C F:PRO99 4.2 53.3 1.0
CD1 F:ILE109 4.2 62.3 1.0
NH2 F:ARG107 4.3 91.0 1.0
CA F:PRO99 4.3 48.1 1.0
C F:TYR98 4.6 52.4 1.0
C08 F:UCK1206 4.6 87.2 1.0
CD2 F:TYR98 4.6 53.1 1.0
NH1 F:ARG107 4.6 1.0 1.0
CG1 F:ILE109 4.7 53.1 1.0
CG F:PRO86 4.7 50.7 1.0
CG F:TYR98 4.9 50.4 1.0
CA F:TYR98 5.0 48.1 1.0
CG F:ARG107 5.0 65.8 1.0

Chlorine binding site 4 out of 8 in 4b95

Go back to Chlorine Binding Sites List in 4b95
Chlorine binding site 4 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1206

b:88.2
occ:1.00
 CL2 F:UCK1206 0.0 88.2 1.0
C19 F:UCK1206 1.7 84.5 1.0
C21 F:UCK1206 2.6 83.1 1.0
C18 F:UCK1206 2.7 82.4 1.0
C17 F:UCK1206 3.1 81.0 1.0
N16 F:UCK1206 3.6 76.6 1.0
O25 F:UCK1206 3.6 82.8 1.0
OH F:TYR98 3.6 61.9 1.0
O15 F:UCK1206 3.8 75.5 1.0
C26 F:UCK1206 3.9 73.9 1.0
C22 F:UCK1206 4.0 82.8 1.0
C24 F:UCK1206 4.0 81.6 1.0
CZ3 F:TRP88 4.3 57.1 1.0
C23 F:UCK1206 4.5 82.1 1.0
OE1 F:GLN96 4.5 96.2 1.0
C05 F:UCK1206 4.6 76.8 1.0
C04 F:UCK1206 4.7 75.5 1.0
CH2 F:TRP88 4.8 59.2 1.0
CE3 F:TRP88 4.9 53.9 1.0
CZ F:TYR98 5.0 58.8 1.0

Chlorine binding site 5 out of 8 in 4b95

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Chlorine binding site 5 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1206

b:83.9
occ:1.00
 CL1 I:UCK1206 0.0 83.9 1.0
C11 I:UCK1206 1.7 76.6 1.0
C13 I:UCK1206 2.7 73.7 1.0
C10 I:UCK1206 2.7 71.9 1.0
O I:PRO99 3.4 57.7 1.0
NE I:ARG107 3.6 84.3 1.0
CG I:PRO86 3.9 49.4 1.0
CD I:PRO99 3.9 54.5 1.0
CB I:TYR98 4.0 44.6 1.0
C14 I:UCK1206 4.0 69.0 1.0
C09 I:UCK1206 4.0 68.1 1.0
CG2 I:ILE109 4.1 48.8 1.0
CD I:ARG107 4.1 64.4 1.0
N I:PRO99 4.2 51.4 1.0
CZ I:ARG107 4.3 0.1 1.0
C I:PRO99 4.4 57.2 1.0
CE2 I:PHE76 4.4 56.6 1.0
CD2 I:PHE76 4.5 53.5 1.0
NH2 I:ARG107 4.5 85.7 1.0
C08 I:UCK1206 4.5 65.4 1.0
CD2 I:TYR98 4.6 44.8 1.0
CB I:PRO99 4.6 54.6 1.0
C I:TYR98 4.6 52.5 1.0
CG I:TYR98 4.7 43.8 1.0
CA I:PRO99 4.7 51.8 1.0
CB I:PRO86 4.7 45.0 1.0
CG I:PRO99 4.7 59.8 1.0
CA I:TYR98 4.9 47.1 1.0
CB I:ILE109 5.0 49.1 1.0
CD I:PRO86 5.0 45.4 1.0

Chlorine binding site 6 out of 8 in 4b95

Go back to Chlorine Binding Sites List in 4b95
Chlorine binding site 6 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl1206

b:73.9
occ:1.00
 CL2 I:UCK1206 0.0 73.9 1.0
C19 I:UCK1206 1.7 68.1 1.0
C21 I:UCK1206 2.6 63.4 1.0
C18 I:UCK1206 2.7 68.0 1.0
C17 I:UCK1206 3.1 68.5 1.0
N16 I:UCK1206 3.4 66.1 1.0
OH I:TYR98 3.6 52.1 1.0
C26 I:UCK1206 3.6 64.9 1.0
O25 I:UCK1206 3.8 70.0 1.0
O15 I:UCK1206 3.9 60.0 1.0
C22 I:UCK1206 4.0 62.1 1.0
C24 I:UCK1206 4.0 65.2 1.0
CZ3 I:TRP88 4.0 54.1 1.0
C23 I:UCK1206 4.5 63.3 1.0
CH2 I:TRP88 4.5 55.2 1.0
C04 I:UCK1206 4.5 64.2 1.0
C05 I:UCK1206 4.6 63.0 1.0
CE3 I:TRP88 4.7 51.7 1.0
CZ I:TYR98 4.9 50.0 1.0

Chlorine binding site 7 out of 8 in 4b95

Go back to Chlorine Binding Sites List in 4b95
Chlorine binding site 7 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1206

b:63.8
occ:1.00
 CL1 L:UCK1206 0.0 63.8 1.0
C11 L:UCK1206 1.8 57.2 1.0
C13 L:UCK1206 2.7 52.8 1.0
C10 L:UCK1206 2.8 54.7 1.0
O L:PRO99 3.7 43.3 1.0
CG1 L:ILE109 3.8 46.0 1.0
CD L:PRO99 3.8 39.1 1.0
CD1 L:ILE109 3.8 61.6 1.0
NE L:ARG107 3.8 76.9 1.0
CB L:TYR98 3.9 38.6 1.0
C14 L:UCK1206 4.0 50.8 1.0
C09 L:UCK1206 4.0 52.9 1.0
N L:PRO99 4.2 37.3 1.0
CG L:PRO86 4.2 53.5 1.0
CD L:ARG107 4.3 64.8 1.0
CD2 L:TYR98 4.3 40.4 1.0
CZ L:ARG107 4.5 77.4 1.0
CG L:TYR98 4.5 39.1 1.0
CE2 L:PHE76 4.5 41.9 1.0
C08 L:UCK1206 4.5 50.4 1.0
CD2 L:PHE76 4.6 40.5 1.0
C L:PRO99 4.6 42.8 1.0
CG L:PRO99 4.7 44.8 1.0
CB L:PRO99 4.7 40.3 1.0
NH2 L:ARG107 4.7 45.3 1.0
C L:TYR98 4.7 42.4 1.0
CA L:PRO99 4.8 37.4 1.0
CB L:PRO86 4.8 47.8 1.0
CA L:TYR98 4.9 40.4 1.0

Chlorine binding site 8 out of 8 in 4b95

Go back to Chlorine Binding Sites List in 4b95
Chlorine binding site 8 out of 8 in the Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Pvhl-Elob-Elob-Eloc COMPLEX_(2S,4R)-1-(2-Chlorophenyl)Carbonyl-N-[(4- Chlorophenyl)Methyl]-4-Oxidanyl-Pyrrolidine-2-Carboxamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1206

b:56.8
occ:1.00
 CL2 L:UCK1206 0.0 56.8 1.0
C19 L:UCK1206 1.7 51.3 1.0
C21 L:UCK1206 2.6 45.2 1.0
C18 L:UCK1206 2.7 53.2 1.0
C17 L:UCK1206 3.0 56.7 1.0
OH L:TYR98 3.4 30.8 1.0
N16 L:UCK1206 3.5 56.5 1.0
O25 L:UCK1206 3.6 59.7 1.0
NE2 L:GLN96 3.8 80.4 1.0
O15 L:UCK1206 3.8 57.0 1.0
C26 L:UCK1206 3.9 53.9 1.0
CZ3 L:TRP88 3.9 43.2 1.0
C22 L:UCK1206 4.0 45.0 1.0
C24 L:UCK1206 4.0 50.1 1.0
CH2 L:TRP88 4.5 44.8 1.0
C23 L:UCK1206 4.5 47.3 1.0
CE3 L:TRP88 4.5 40.3 1.0
C04 L:UCK1206 4.6 57.0 1.0
C05 L:UCK1206 4.6 55.5 1.0
CZ L:TYR98 4.7 38.0 1.0
CD L:GLN96 4.8 89.5 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 HIF1ALPHA Angew.Chem.Int.Ed.Engl. V. 51 11463 2012.
ISSN: ISSN 1433-7851
PubMed: 23065727
DOI: 10.1002/ANIE.201206231
Page generated: Sun Jul 21 09:50:12 2024

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