Chlorine in PDB 7m2k: CDC34A-Ubiquitin-2AB Inhibitor Complex

Enzymatic activity of CDC34A-Ubiquitin-2AB Inhibitor Complex

All present enzymatic activity of CDC34A-Ubiquitin-2AB Inhibitor Complex:
2.3.2.23; 2.3.2.24;

Protein crystallography data

The structure of CDC34A-Ubiquitin-2AB Inhibitor Complex, PDB code: 7m2k was solved by D.F.Ceccarelli, D.St-Cyr, M.Tyers, F.Sicheri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 67.30 / 2.47
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 55.8, 72, 76.5, 70.14, 79.12, 80.42
R / Rfree (%) 21.9 / 27.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the CDC34A-Ubiquitin-2AB Inhibitor Complex (pdb code 7m2k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the CDC34A-Ubiquitin-2AB Inhibitor Complex, PDB code: 7m2k:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 7m2k

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Chlorine binding site 1 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:81.7
occ:1.00
 CL1 A:GZM201 0.0 81.7 1.0
C26 A:GZM201 1.7 57.1 1.0
C18 A:GZM201 2.7 65.7 1.0
C27 A:GZM201 2.7 48.2 1.0
CD1 A:ILE128 3.6 61.7 1.0
CA B:GLY47 3.7 74.8 1.0
O B:GLY47 3.9 55.0 1.0
CG1 A:ILE128 3.9 55.4 1.0
C17 A:GZM201 4.0 62.6 1.0
C15 A:GZM201 4.0 65.8 1.0
CE1 A:PHE28 4.1 55.6 1.0
CG A:PRO48 4.2 62.6 1.0
CG2 A:ILE128 4.3 55.9 1.0
C B:GLY47 4.3 72.2 1.0
CD A:PRO48 4.3 61.4 1.0
O A:PHE46 4.4 65.0 1.0
C16 A:GZM201 4.5 57.3 1.0
CB A:ILE128 4.6 57.2 1.0
O A:GLU26 4.6 71.7 1.0
N B:GLY47 4.8 76.5 1.0
CB A:PRO48 4.9 57.7 1.0
CD1 A:PHE28 4.9 56.2 1.0
CG2 A:ILE45 5.0 59.2 1.0

Chlorine binding site 2 out of 8 in 7m2k

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Chlorine binding site 2 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:64.9
occ:1.00
 CL2 A:GZM201 0.0 64.9 1.0
C17 A:GZM201 1.7 62.6 1.0
C18 A:GZM201 2.7 65.7 1.0
C16 A:GZM201 2.7 57.3 1.0
CE2 A:PHE58 3.2 67.3 1.0
CD2 A:PHE58 3.5 57.7 1.0
C26 A:GZM201 4.0 57.1 1.0
C15 A:GZM201 4.0 65.8 1.0
CD2 A:TYR53 4.0 48.8 1.0
CB A:TYR53 4.1 49.8 1.0
CA A:GLY47 4.1 54.7 1.0
CZ A:PHE58 4.1 57.7 1.0
CG A:TYR53 4.1 51.4 1.0
CD1 A:LEU131 4.2 57.4 1.0
CG2 A:ILE45 4.3 59.2 1.0
N A:GLY47 4.4 65.5 1.0
CG A:PHE58 4.4 58.2 1.0
C27 A:GZM201 4.5 48.2 1.0
C A:PHE46 4.7 65.2 1.0
CE2 A:TYR53 4.8 56.8 1.0
CD A:PRO48 4.8 61.4 1.0
O A:PHE46 4.8 65.0 1.0
CD1 A:TYR53 4.9 56.0 1.0
CD2 A:LEU131 4.9 57.8 1.0
CE1 A:PHE58 5.0 57.9 1.0

Chlorine binding site 3 out of 8 in 7m2k

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Chlorine binding site 3 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:68.5
occ:1.00
 CL1 C:GZM201 0.0 68.5 1.0
C26 C:GZM201 1.7 58.5 1.0
C18 C:GZM201 2.7 71.0 1.0
C27 C:GZM201 2.8 54.1 1.0
CA D:GLY47 3.8 56.9 1.0
CG C:PRO48 3.8 60.2 1.0
O D:GLY47 3.9 60.3 1.0
CG1 C:ILE128 3.9 55.2 1.0
C17 C:GZM201 4.0 70.6 1.0
C15 C:GZM201 4.0 60.1 1.0
CE2 C:PHE28 4.1 67.6 1.0
CG2 C:ILE128 4.3 56.4 1.0
CD C:PRO48 4.3 70.3 1.0
C D:GLY47 4.3 59.8 1.0
O C:PHE46 4.4 62.0 1.0
CD1 C:ILE128 4.5 55.4 1.0
C16 C:GZM201 4.6 57.0 1.0
O C:GLU26 4.6 79.1 1.0
CB C:ILE128 4.6 58.6 1.0
CZ C:PHE28 4.8 69.0 1.0
CB C:PRO48 4.9 62.3 1.0
CD2 C:PHE28 4.9 56.0 1.0

Chlorine binding site 4 out of 8 in 7m2k

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Chlorine binding site 4 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl201

b:113.5
occ:1.00
 CL2 C:GZM201 0.0 113.5 1.0
C17 C:GZM201 1.7 70.6 1.0
C18 C:GZM201 2.6 71.0 1.0
C16 C:GZM201 2.7 57.0 1.0
CD2 C:TYR53 3.5 51.0 1.0
CG2 C:ILE45 3.5 68.4 1.0
CE1 C:PHE58 3.5 53.0 1.0
CD1 C:PHE58 3.6 53.5 1.0
CG C:TYR53 3.9 51.0 1.0
C26 C:GZM201 4.0 58.5 1.0
C15 C:GZM201 4.0 60.1 1.0
CB C:TYR53 4.0 51.5 1.0
CZ C:PHE58 4.2 52.7 1.0
CE2 C:TYR53 4.2 50.8 1.0
CD1 C:LEU131 4.2 53.4 1.0
CA C:GLY47 4.2 67.7 1.0
CG C:PHE58 4.3 59.5 1.0
C27 C:GZM201 4.5 54.1 1.0
N C:GLY47 4.5 80.7 1.0
CE2 C:PHE58 4.8 52.9 1.0
CD2 C:PHE58 4.9 65.6 1.0
C C:PHE46 4.9 71.6 1.0
CD C:PRO48 4.9 70.3 1.0
CD2 C:LEU131 4.9 54.0 1.0
CE C:MET81 4.9 73.3 1.0
O C:PHE46 4.9 62.0 1.0
CD1 C:TYR53 4.9 54.8 1.0
CB C:ILE45 5.0 60.8 1.0

Chlorine binding site 5 out of 8 in 7m2k

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Chlorine binding site 5 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:81.8
occ:1.00
 CL1 E:GZM201 0.0 81.8 1.0
C26 E:GZM201 1.7 65.8 1.0
C18 E:GZM201 2.6 62.0 1.0
C27 E:GZM201 2.7 66.6 1.0
CA F:GLY47 3.5 69.6 1.0
O F:GLY47 3.8 72.2 1.0
CG E:PRO48 3.9 72.6 1.0
C17 E:GZM201 3.9 65.1 1.0
C15 E:GZM201 4.0 63.9 1.0
CE1 E:PHE28 4.1 59.4 1.0
C F:GLY47 4.1 69.6 1.0
CG2 E:ILE128 4.2 52.6 1.0
CD E:PRO48 4.3 64.6 1.0
O E:PHE46 4.3 69.3 1.0
CG1 E:ILE128 4.4 52.5 1.0
C16 E:GZM201 4.5 55.4 1.0
O E:GLU26 4.5 81.2 1.0
CD1 E:PHE28 4.7 73.3 1.0
N F:GLY47 4.7 83.5 1.0
CA E:GLY27 4.8 75.4 1.0
CB E:ILE128 4.8 56.5 1.0
CB E:PRO48 4.9 70.2 1.0
CG2 E:ILE45 5.0 63.6 1.0
O E:GLY27 5.0 74.7 1.0

Chlorine binding site 6 out of 8 in 7m2k

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Chlorine binding site 6 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl201

b:61.5
occ:1.00
 CL2 E:GZM201 0.0 61.5 1.0
C17 E:GZM201 1.8 65.1 1.0
C18 E:GZM201 2.7 62.0 1.0
C16 E:GZM201 2.8 55.4 1.0
CE2 E:PHE58 3.2 70.7 1.0
CD2 E:PHE58 3.3 55.6 1.0
CD2 E:TYR53 3.7 53.4 1.0
CB E:TYR53 3.9 55.2 1.0
CG E:TYR53 3.9 56.7 1.0
C26 E:GZM201 4.0 65.8 1.0
CZ E:PHE58 4.0 66.1 1.0
C15 E:GZM201 4.1 63.9 1.0
CG2 E:ILE45 4.2 63.6 1.0
CG E:PHE58 4.2 56.7 1.0
CA E:GLY47 4.2 60.9 1.0
CD1 E:LEU131 4.4 59.8 1.0
N E:GLY47 4.5 59.2 1.0
CE2 E:TYR53 4.5 52.0 1.0
C27 E:GZM201 4.6 66.6 1.0
C E:PHE46 4.8 62.7 1.0
CD2 E:LEU131 4.8 63.0 1.0
CE1 E:PHE58 4.8 58.1 1.0
CD1 E:TYR53 4.8 59.7 1.0
CD1 E:PHE58 4.9 54.6 1.0
O E:PHE46 4.9 69.3 1.0
CD E:PRO48 5.0 64.6 1.0

Chlorine binding site 7 out of 8 in 7m2k

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Chlorine binding site 7 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:75.2
occ:1.00
 CL1 G:GZM201 0.0 75.2 1.0
C26 G:GZM201 1.7 72.5 1.0
C18 G:GZM201 2.7 55.9 1.0
C27 G:GZM201 2.7 70.8 1.0
CG2 G:ILE128 3.4 79.2 1.0
CA H:GLY47 3.5 72.3 1.0
O H:GLY47 3.7 71.7 1.0
C17 G:GZM201 4.0 64.5 1.0
C15 G:GZM201 4.0 73.5 1.0
CD1 G:ILE128 4.0 58.7 1.0
C H:GLY47 4.1 62.5 1.0
CE1 G:PHE28 4.2 65.5 1.0
CG G:PRO48 4.3 81.1 1.0
CD G:PRO48 4.3 73.5 1.0
CG1 G:ILE128 4.3 63.5 1.0
O G:PHE46 4.4 67.1 1.0
CB G:ILE128 4.4 61.5 1.0
O G:GLU26 4.5 72.8 1.0
C16 G:GZM201 4.5 70.5 1.0
CB G:PRO48 4.5 73.2 1.0
N H:GLY47 4.8 77.7 1.0
CD1 G:PHE28 4.8 68.0 1.0

Chlorine binding site 8 out of 8 in 7m2k

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Chlorine binding site 8 out of 8 in the CDC34A-Ubiquitin-2AB Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of CDC34A-Ubiquitin-2AB Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl201

b:60.8
occ:1.00
 CL2 G:GZM201 0.0 60.8 1.0
C17 G:GZM201 1.8 64.5 1.0
C18 G:GZM201 2.8 55.9 1.0
C16 G:GZM201 2.9 70.5 1.0
CE2 G:PHE58 3.1 62.3 1.0
CD2 G:PHE58 3.3 64.8 1.0
CG2 G:ILE45 3.5 59.7 1.0
CD2 G:TYR53 3.9 55.0 1.0
CB G:TYR53 3.9 58.5 1.0
CZ G:PHE58 3.9 58.1 1.0
CD1 G:LEU131 4.0 71.1 1.0
CA G:GLY47 4.0 62.9 1.0
CG G:TYR53 4.0 65.8 1.0
C26 G:GZM201 4.1 72.5 1.0
C15 G:GZM201 4.2 73.5 1.0
CG G:PHE58 4.2 61.9 1.0
N G:GLY47 4.3 68.5 1.0
C G:PHE46 4.6 60.4 1.0
C27 G:GZM201 4.6 70.8 1.0
O G:PHE46 4.7 67.1 1.0
CD G:PRO48 4.7 73.5 1.0
CE2 G:TYR53 4.7 54.2 1.0
CB G:ILE45 4.8 60.4 1.0
CE1 G:PHE58 4.8 59.6 1.0
CD1 G:PHE58 4.9 55.6 1.0
CD1 G:TYR53 5.0 57.3 1.0

Reference:

D.St-Cyrt, D.F.Ceccarelli, S.Orlicky, A.M.Van Der Sloot, X.Tang, S.Kelso, S.Moore, C.James, G.Posternak, J.Coulombe-Huntington, T.Bertomeu, A.Marinier, F.Sicheri, M.Tyers. Identification and Optimization of Molecular Glue Compounds That Inhibit A Noncovalent E2 Enzyme-Ubiquitin Complex Sci Adv V. 7 2021.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ABI5797
Page generated: Tue Jul 30 00:22:48 2024

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