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Chlorine in PDB 5cu0: Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound

Enzymatic activity of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound

All present enzymatic activity of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound, PDB code: 5cu0 was solved by P.Brear, C.De Fusco, K.H.Georgiou, D.Spring, M.Hyvonen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 167.27 / 2.18
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 64.698, 68.272, 334.537, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 23.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound (pdb code 5cu0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound, PDB code: 5cu0:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5cu0

Go back to Chlorine Binding Sites List in 5cu0
Chlorine binding site 1 out of 4 in the Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:70.4
occ:1.00
 CL A:54R401 0.0 70.4 1.0
C10 A:54R401 1.7 60.0 1.0
C11 A:54R401 2.7 53.9 1.0
C9 A:54R401 2.7 54.2 1.0
C17 A:54R401 2.9 59.3 1.0
C12 A:54R401 3.1 55.2 1.0
SD A:MET221 3.3 31.8 1.0
CE A:MET221 3.5 28.4 1.0
CA A:PRO159 3.6 24.8 1.0
CB A:VAL162 3.8 32.4 1.0
CB A:PRO159 3.9 26.4 1.0
CG2 A:VAL162 4.0 32.4 1.0
C6 A:54R401 4.0 51.2 1.0
C8 A:54R401 4.0 51.5 1.0
C16 A:54R401 4.1 62.8 1.0
CG1 A:VAL162 4.1 33.0 1.0
CG A:MET221 4.2 27.7 1.0
N A:PRO159 4.2 25.8 1.0
CG A:PRO159 4.3 31.1 1.0
CD1 A:ILE140 4.3 21.1 1.0
C13 A:54R401 4.3 55.9 1.0
C7 A:54R401 4.5 51.4 1.0
O A:PRO159 4.5 33.5 1.0
C A:PRO159 4.6 32.2 1.0
O A:LYS158 4.6 29.2 1.0
C A:LYS158 4.7 28.4 1.0
CB A:MET221 4.7 19.8 1.0
CD A:PRO159 4.8 27.5 1.0

Chlorine binding site 2 out of 4 in 5cu0

Go back to Chlorine Binding Sites List in 5cu0
Chlorine binding site 2 out of 4 in the Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:20.0
occ:0.50
 CL A:54R402 0.0 20.0 0.5
C10 A:54R402 1.7 20.0 0.5
C11 A:54R402 2.7 20.0 0.5
C9 A:54R402 2.7 20.0 0.5
C12 A:54R402 3.1 20.0 0.5
C17 A:54R402 3.3 20.0 0.5
C6 A:54R402 4.0 20.0 0.5
CD2 A:LEU41 4.0 37.6 1.0
C8 A:54R402 4.0 20.0 0.5
CG1 A:VAL67 4.0 32.2 1.0
C13 A:54R402 4.0 20.0 0.5
CB A:TYR39 4.2 32.4 1.0
CG A:LEU41 4.3 36.5 1.0
O A:GLN36 4.3 37.5 1.0
C16 A:54R402 4.4 20.0 0.5
CG2 A:VAL101 4.4 41.5 1.0
C7 A:54R402 4.5 20.0 0.5
CD1 A:LEU41 4.6 35.9 1.0
CG2 A:VAL67 4.6 34.5 1.0
O A:TYR39 4.7 40.0 1.0
CB A:VAL67 4.8 33.7 1.0
C14 A:54R402 4.9 20.0 0.5
CB A:GLN36 5.0 37.3 1.0

Chlorine binding site 3 out of 4 in 5cu0

Go back to Chlorine Binding Sites List in 5cu0
Chlorine binding site 3 out of 4 in the Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:93.7
occ:1.00
 CL B:54R401 0.0 93.7 1.0
C10 B:54R401 1.7 82.1 1.0
C11 B:54R401 2.7 76.1 1.0
C9 B:54R401 2.7 77.9 1.0
C17 B:54R401 2.9 73.5 1.0
C12 B:54R401 3.1 73.8 1.0
CE B:MET221 3.4 45.9 1.0
SD B:MET221 3.6 48.2 1.0
CB B:VAL162 3.6 37.1 1.0
CD1 B:ILE140 3.7 44.4 1.0
CG1 B:VAL162 3.8 37.2 1.0
CG2 B:VAL162 3.8 37.5 1.0
C6 B:54R401 4.0 73.0 1.0
C8 B:54R401 4.0 78.3 1.0
C16 B:54R401 4.1 72.4 1.0
CA B:PRO159 4.1 37.6 1.0
C13 B:54R401 4.4 71.6 1.0
C7 B:54R401 4.5 76.1 1.0
CB B:PRO159 4.5 39.6 1.0
CG B:MET221 4.6 46.7 1.0
N B:PRO159 4.8 38.0 1.0
CG B:PRO159 4.8 44.9 1.0
O B:PRO159 4.9 34.6 1.0
CB B:MET221 5.0 44.1 1.0
O B:LYS158 5.0 37.6 1.0

Chlorine binding site 4 out of 4 in 5cu0

Go back to Chlorine Binding Sites List in 5cu0
Chlorine binding site 4 out of 4 in the Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of CK2ALPHA with 2-Hydroxy-5-Methylbenzoic Acid and N-(3-(3-Chloro-4-(Phenyl)Benzylamino)Propyl)Acetamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:20.0
occ:0.50
 CL B:54R402 0.0 20.0 0.5
C10 B:54R402 1.7 20.0 0.5
C11 B:54R402 2.7 20.0 0.5
C9 B:54R402 2.7 20.0 0.5
C12 B:54R402 3.1 20.0 0.5
C17 B:54R402 3.4 20.0 0.5
C6 B:54R402 4.0 20.0 0.5
C13 B:54R402 4.0 20.0 0.5
C8 B:54R402 4.0 20.0 0.5
CG1 B:VAL67 4.1 37.0 1.0
CD2 B:LEU41 4.1 59.4 1.0
CB B:TYR39 4.1 44.6 1.0
O B:GLN36 4.3 50.0 1.0
CG2 B:VAL101 4.3 45.5 1.0
CG B:LEU41 4.4 59.1 1.0
C16 B:54R402 4.4 20.0 0.5
C7 B:54R402 4.5 20.0 0.5
CG2 B:VAL67 4.6 38.3 1.0
CD1 B:LEU41 4.7 59.5 1.0
O B:TYR39 4.7 53.5 1.0
CB B:GLN36 4.8 48.2 1.0
CB B:VAL67 4.8 38.6 1.0
CG B:TYR39 4.9 43.7 1.0
C14 B:54R402 4.9 20.0 0.5
CA B:GLN36 4.9 46.6 1.0
CD2 B:TYR39 5.0 44.0 1.0

Reference:

C.De Fusco, P.Brear, J.Iegre, K.H.Georgiou, H.F.Sore, M.Hyvonen, D.R.Spring. A Fragment-Based Approach Leading to the Discovery of A Novel Binding Site and the Selective CK2 Inhibitor CAM4066. Bioorg. Med. Chem. V. 25 3471 2017.
ISSN: ESSN 1464-3391
PubMed: 28495381
DOI: 10.1016/J.BMC.2017.04.037
Page generated: Fri Jul 26 06:17:11 2024

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