Chlorine in PDB 6r1k: Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C

Protein crystallography data

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C, PDB code: 6r1k was solved by C.Heim, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.46 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.230, 60.080, 88.520, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.2

Other elements in 6r1k:

The structure of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C (pdb code 6r1k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C, PDB code: 6r1k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6r1k

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Chlorine binding site 1 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:59.8
occ:1.00
CL1 A:JPB202 0.0 59.8 1.0
C7 A:JPB202 1.7 58.3 1.0
C8 A:JPB202 2.7 63.2 1.0
C6 A:JPB202 2.7 55.0 1.0
C5 A:JPB202 3.1 47.7 1.0
N2 A:JPB202 3.3 43.8 1.0
O1 A:JPB202 3.4 40.3 1.0
CD A:PRO51 3.5 44.7 1.0
CD2 A:PHE77 3.7 50.3 1.0
CG A:PRO51 3.8 46.9 1.0
O A:HOH336 3.9 62.0 1.0
O3 A:JPB202 3.9 50.8 1.0
CZ2 A:TRP85 4.0 39.3 1.0
C9 A:JPB202 4.0 66.1 1.0
C1 A:JPB202 4.0 39.5 1.0
C11 A:JPB202 4.0 59.8 1.0
CH2 A:TRP85 4.2 38.5 1.0
C4 A:JPB202 4.3 38.8 1.0
CE2 A:PHE77 4.3 52.2 1.0
CG A:PHE77 4.4 47.9 1.0
C10 A:JPB202 4.5 63.4 1.0
CB A:PHE77 4.5 43.9 1.0
CB A:ASN50 4.8 40.9 1.0
O A:GLU76 4.9 41.7 1.0
N A:PRO51 4.9 44.5 1.0
CE2 A:TRP85 4.9 37.5 1.0
CB A:PRO51 5.0 48.6 1.0

Chlorine binding site 2 out of 12 in 6r1k

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Chlorine binding site 2 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:79.3
occ:1.00
CL2 A:JPB202 0.0 79.3 1.0
C9 A:JPB202 1.7 66.1 1.0
C8 A:JPB202 2.7 63.2 1.0
C10 A:JPB202 2.7 63.4 1.0
C7 A:JPB202 4.0 58.3 1.0
C11 A:JPB202 4.0 59.8 1.0
C6 A:JPB202 4.5 55.0 1.0

Chlorine binding site 3 out of 12 in 6r1k

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Chlorine binding site 3 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:64.5
occ:1.00
CL3 A:JPB202 0.0 64.5 1.0
C11 A:JPB202 1.8 59.8 1.0
C10 A:JPB202 2.7 63.4 1.0
C6 A:JPB202 2.7 55.0 1.0
C5 A:JPB202 3.0 47.7 1.0
O3 A:JPB202 3.2 50.8 1.0
NE1 A:TRP99 3.4 33.8 1.0
CG1 A:ILE87 3.7 37.8 1.0
N2 A:JPB202 3.8 43.8 1.0
CE1 A:HIS96 3.9 35.1 1.0
CD1 A:ILE87 3.9 41.1 1.0
C9 A:JPB202 4.0 66.1 1.0
C7 A:JPB202 4.0 58.3 1.0
CE2 A:TRP99 4.2 31.4 1.0
CZ2 A:TRP99 4.2 35.5 1.0
O A:HOH343 4.2 56.4 1.0
NE2 A:HIS96 4.2 34.0 1.0
CD1 A:TRP99 4.5 31.9 1.0
C8 A:JPB202 4.5 63.2 1.0
ND1 A:HIS96 4.7 35.8 1.0
C4 A:JPB202 4.8 38.8 1.0
CZ3 A:TRP85 4.8 37.8 1.0
CG2 A:ILE87 5.0 37.1 1.0
CB A:ILE87 5.0 36.1 1.0

Chlorine binding site 4 out of 12 in 6r1k

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Chlorine binding site 4 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:56.6
occ:1.00
CL1 B:JPB202 0.0 56.6 1.0
C7 B:JPB202 1.8 46.8 1.0
C8 B:JPB202 2.7 48.3 1.0
C6 B:JPB202 2.7 43.0 1.0
C5 B:JPB202 3.0 41.0 1.0
O B:HOH350 3.1 52.2 1.0
O3 B:JPB202 3.2 38.1 1.0
NE1 B:TRP99 3.4 33.1 1.0
CG1 B:ILE87 3.8 37.7 1.0
N2 B:JPB202 3.9 35.5 1.0
CD1 B:ILE87 3.9 42.0 1.0
C9 B:JPB202 4.0 49.5 1.0
CZ2 B:TRP99 4.0 33.6 1.0
C11 B:JPB202 4.0 46.2 1.0
CE2 B:TRP99 4.0 29.9 1.0
CE1 B:HIS96 4.2 38.6 1.0
CD1 B:TRP99 4.5 30.9 1.0
NE2 B:HIS96 4.5 34.0 1.0
C10 B:JPB202 4.5 49.1 1.0
CZ3 B:TRP85 4.8 33.9 1.0
C4 B:JPB202 4.8 33.6 1.0

Chlorine binding site 5 out of 12 in 6r1k

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Chlorine binding site 5 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:59.4
occ:1.00
CL2 B:JPB202 0.0 59.4 1.0
C9 B:JPB202 1.7 49.5 1.0
C10 B:JPB202 2.6 49.1 1.0
C8 B:JPB202 2.7 48.3 1.0
O B:HOH355 3.5 69.9 1.0
C11 B:JPB202 3.9 46.2 1.0
C7 B:JPB202 4.0 46.8 1.0
N1 B:JPB203 4.2 91.4 1.0
C1 B:JPB203 4.4 86.3 1.0
O1 B:JPB203 4.5 77.9 1.0
C6 B:JPB202 4.5 43.0 1.0
CL3 B:JPB203 4.7 97.5 1.0
N2 B:JPB203 5.0 88.1 1.0

Chlorine binding site 6 out of 12 in 6r1k

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Chlorine binding site 6 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl202

b:47.8
occ:1.00
CL3 B:JPB202 0.0 47.8 1.0
C11 B:JPB202 1.7 46.2 1.0
C10 B:JPB202 2.6 49.1 1.0
C6 B:JPB202 2.7 43.0 1.0
C5 B:JPB202 3.1 41.0 1.0
N2 B:JPB202 3.3 35.5 1.0
O1 B:JPB202 3.5 35.3 1.0
CD B:PRO51 3.6 35.8 1.0
O3 B:JPB203 3.7 78.8 1.0
CL3 B:JPB203 3.8 97.5 1.0
CZ2 B:TRP85 3.9 34.4 1.0
C9 B:JPB202 3.9 49.5 1.0
O3 B:JPB202 3.9 38.1 1.0
CD2 B:PHE77 3.9 47.5 1.0
CG B:PRO51 4.0 37.5 1.0
C7 B:JPB202 4.0 46.8 1.0
C1 B:JPB202 4.1 34.6 1.0
CH2 B:TRP85 4.1 37.2 1.0
C4 B:JPB202 4.3 33.6 1.0
C8 B:JPB202 4.5 48.3 1.0
C5 B:JPB203 4.5 81.3 1.0
CE2 B:PHE77 4.6 49.0 1.0
CB B:PHE77 4.7 42.5 1.0
CG B:PHE77 4.7 46.1 1.0
CB B:ASN50 4.7 31.1 1.0
C11 B:JPB203 4.8 86.5 1.0
CE2 B:TRP85 4.9 32.7 1.0
N B:PRO51 4.9 33.4 1.0
O B:GLU76 4.9 38.0 1.0

Chlorine binding site 7 out of 12 in 6r1k

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Chlorine binding site 7 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:74.5
occ:1.00
CL1 B:JPB203 0.0 74.5 1.0
C7 B:JPB203 1.7 84.3 1.0
C8 B:JPB203 2.7 85.9 1.0
C6 B:JPB203 2.7 84.5 1.0
C5 B:JPB203 3.0 81.3 1.0
N2 B:JPB203 3.3 88.1 1.0
O3 B:JPB203 3.7 78.8 1.0
N B:ALA52 3.7 34.4 1.0
CA B:ALA52 3.7 35.3 1.0
C B:PRO51 3.8 35.7 1.0
C4 B:JPB203 3.8 88.8 1.0
O B:PRO51 3.8 39.2 1.0
CB B:ALA52 3.9 35.5 1.0
C9 B:JPB203 4.0 88.8 1.0
C11 B:JPB203 4.0 86.5 1.0
CB B:PRO51 4.3 37.9 1.0
C3 B:JPB203 4.4 88.2 1.0
C10 B:JPB203 4.5 87.2 1.0
CA B:PRO51 4.7 36.1 1.0

Chlorine binding site 8 out of 12 in 6r1k

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Chlorine binding site 8 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:99.2
occ:1.00
CL2 B:JPB203 0.0 99.2 1.0
C9 B:JPB203 1.7 88.8 1.0
C10 B:JPB203 2.7 87.2 1.0
C8 B:JPB203 2.7 85.9 1.0
C11 B:JPB203 4.0 86.5 1.0
C7 B:JPB203 4.0 84.3 1.0
CZ B:PHE77 4.3 49.0 1.0
C6 B:JPB203 4.5 84.5 1.0
CE2 B:PHE77 4.9 49.0 1.0

Chlorine binding site 9 out of 12 in 6r1k

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Chlorine binding site 9 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:97.5
occ:1.00
CL3 B:JPB203 0.0 97.5 1.0
C11 B:JPB203 1.7 86.5 1.0
C10 B:JPB203 2.7 87.2 1.0
C6 B:JPB203 2.7 84.5 1.0
C5 B:JPB203 3.1 81.3 1.0
O3 B:JPB203 3.5 78.8 1.0
C10 B:JPB202 3.6 49.1 1.0
CL3 B:JPB202 3.8 47.8 1.0
CE2 B:PHE77 3.8 49.0 1.0
N2 B:JPB203 3.9 88.1 1.0
C9 B:JPB203 3.9 88.8 1.0
C7 B:JPB203 4.0 84.3 1.0
C11 B:JPB202 4.3 46.2 1.0
CD2 B:PHE77 4.3 47.5 1.0
C8 B:JPB203 4.5 85.9 1.0
C9 B:JPB202 4.7 49.5 1.0
CL2 B:JPB202 4.7 59.4 1.0
CZ B:PHE77 4.8 49.0 1.0
CG B:PRO51 4.9 37.5 1.0

Chlorine binding site 10 out of 12 in 6r1k

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Chlorine binding site 10 out of 12 in the Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Cereblon Isoform 4 From Magnetospirillum Gryphiswaldense in Complex with Compound 7C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl202

b:86.1
occ:1.00
CL1 C:JPB202 0.0 86.1 1.0
C7 C:JPB202 1.7 85.8 1.0
C8 C:JPB202 2.7 85.5 1.0
C6 C:JPB202 2.8 80.7 1.0
C5 C:JPB202 3.1 73.2 1.0
N2 C:JPB202 3.4 67.7 1.0
O1 C:JPB202 3.5 63.3 1.0
O3 C:JPB202 3.7 69.9 1.0
CD C:PRO51 3.7 64.7 1.0
CG C:PRO51 3.7 68.9 1.0
CZ2 C:TRP85 3.9 65.9 1.0
C9 C:JPB202 4.0 85.3 1.0
C1 C:JPB202 4.0 66.2 1.0
C11 C:JPB202 4.0 84.1 1.0
CB C:PHE77 4.1 74.5 1.0
O C:GLU76 4.2 66.8 1.0
C4 C:JPB202 4.3 64.3 1.0
CH2 C:TRP85 4.5 63.8 1.0
C10 C:JPB202 4.5 82.8 1.0
CG C:PHE77 4.8 78.5 1.0
CE2 C:TRP85 4.8 64.0 1.0
C C:GLU76 4.8 70.5 1.0
CD2 C:PHE77 5.0 79.4 1.0

Reference:

C.Heim, D.Pliatsika, F.Mousavizadeh, K.Bar, B.Hernandez Alvarez, A.Giannis, M.D.Hartmann. De-Novo Design of Cereblon (Crbn) Effectors Guided By Natural Hydrolysis Products of Thalidomide Derivatives. J.Med.Chem. V. 62 6615 2019.
ISSN: ISSN 0022-2623
PubMed: 31251063
DOI: 10.1021/ACS.JMEDCHEM.9B00454
Page generated: Sat Dec 12 13:35:22 2020

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