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Chlorine in PDB 6v6l: Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One

Enzymatic activity of Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One

All present enzymatic activity of Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One:
2.7.11.1; 2.7.11.26;

Protein crystallography data

The structure of Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One, PDB code: 6v6l was solved by D.E.Bussiere, E.Fang, W.Shu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.17 / 2.19
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.080, 64.760, 58.250, 90.00, 100.13, 90.00
R / Rfree (%) 20.3 / 23.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One (pdb code 6v6l). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One, PDB code: 6v6l:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6v6l

Go back to Chlorine Binding Sites List in 6v6l
Chlorine binding site 1 out of 2 in the Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:28.4
occ:1.00
 CL1 A:QQA501 0.0 28.4 1.0
C27 A:QQA501 1.8 26.2 1.0
C26 A:QQA501 2.7 25.9 1.0
C19 A:QQA501 2.8 27.1 1.0
C17 A:QQA501 3.1 25.8 1.0
C32 A:QQA501 3.3 28.9 1.0
N20 A:QQA501 3.4 29.4 1.0
C16 A:QQA501 3.4 26.9 1.0
N A:GLY63 3.5 37.8 1.0
CG2 A:ILE62 3.5 37.5 1.0
CA A:GLY63 3.6 40.6 1.0
CZ A:PHE67 3.9 40.3 1.0
CB A:ILE62 3.9 36.3 1.0
C A:ILE62 4.0 40.2 1.0
CB A:VAL70 4.0 25.8 1.0
N18 A:QQA501 4.0 22.9 1.0
C25 A:QQA501 4.0 25.7 1.0
C23 A:QQA501 4.1 28.6 1.0
C A:GLY63 4.2 43.7 1.0
C28 A:QQA501 4.2 29.9 1.0
CE1 A:PHE67 4.3 38.3 1.0
O A:GLY63 4.3 41.2 1.0
O A:ILE62 4.4 37.7 1.0
C15 A:QQA501 4.4 24.1 1.0
C31 A:QQA501 4.5 29.9 1.0
CG2 A:VAL70 4.5 25.2 1.0
CG1 A:VAL70 4.5 25.2 1.0
C24 A:QQA501 4.6 27.7 1.0
CA A:ILE62 4.6 37.7 1.0
N30 A:QQA501 4.6 31.0 1.0
C5 A:QQA501 4.6 25.1 1.0
CE2 A:PHE67 4.6 42.0 1.0
O36 A:QQA501 4.8 29.7 1.0
C6 A:QQA501 4.8 26.1 1.0
C11 A:QQA501 4.9 22.1 1.0
O A:VAL70 4.9 26.1 1.0
C29 A:QQA501 4.9 30.2 1.0

Chlorine binding site 2 out of 2 in 6v6l

Go back to Chlorine Binding Sites List in 6v6l
Chlorine binding site 2 out of 2 in the Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Structure of Human Glycogen Synthase Kinase Beta with 1-(6-((2-((6- Amino-5-Nitropyridin-2-Yl)Amino)Ethyl)Amino)-2-(2,4-Dichlorophenyl) Pyridin-3-Yl)-4-Methylpiperazin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:26.1
occ:1.00
 CL2 A:QQA501 0.0 26.1 1.0
C25 A:QQA501 1.8 25.7 1.0
C26 A:QQA501 2.7 25.9 1.0
C24 A:QQA501 2.8 27.7 1.0
CD2 A:PHE67 3.6 41.4 1.0
CB A:ASP200 3.7 21.4 1.0
O21 A:QQA501 3.7 24.6 1.0
CG A:PHE67 3.8 38.6 1.0
O A:HOH719 3.8 40.7 1.0
CG A:ASP200 3.9 33.8 1.0
C27 A:QQA501 4.0 26.2 1.0
OD1 A:ASN186 4.0 26.9 1.0
C23 A:QQA501 4.0 28.6 1.0
CB A:PHE67 4.0 39.2 1.0
OD2 A:ASP200 4.1 44.7 1.0
CE2 A:PHE67 4.1 42.0 1.0
CD1 A:PHE67 4.4 37.7 1.0
OD1 A:ASP200 4.4 34.9 1.0
SG A:CYS199 4.5 21.9 1.0
C19 A:QQA501 4.5 27.1 1.0
NZ A:LYS85 4.6 26.2 1.0
CA A:ASP200 4.7 22.1 1.0
CG2 A:VAL70 4.7 25.2 1.0
CZ A:PHE67 4.7 40.3 1.0
N12 A:QQA501 4.8 26.2 1.0
C6 A:QQA501 4.8 26.1 1.0
CD A:LYS85 4.9 25.2 1.0
CE1 A:PHE67 4.9 38.3 1.0

Reference:

S.Ramurthy, K.B.Pfister, R.S.Boyce, S.P.Brown, A.Q.Costales, M.Desai, E.Fang, B.H.Levine, S.C.Ng, J.M.Nuss, D.B.Ring, C.M.Shafer, W.Shu, S.Subramanian, A.S.Wagman, H.Wang, D.E.Bussiere. Discovery and Optimization of Novel Pyridines As Highly Potent and Selective Glycogen Synthase Kinase 3 Inhibitors To Be Published.
Page generated: Sat Jul 12 20:45:23 2025

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