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Chlorine in PDB 8gyd: Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16

Enzymatic activity of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16

All present enzymatic activity of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16:
2.5.1.18;

Protein crystallography data

The structure of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16, PDB code: 8gyd was solved by X.Wen, R.Jin, H.Hu, J.Zhu, W.Song, X.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.90 / 1.70
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 64.149, 64.149, 227.652, 90, 90, 120
R / Rfree (%) 19.3 / 21.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 (pdb code 8gyd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16, PDB code: 8gyd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8gyd

Go back to Chlorine Binding Sites List in 8gyd
Chlorine binding site 1 out of 6 in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:39.3
occ:1.00
 CL1 A:0IH301 0.0 39.3 1.0
C7 A:0IH301 1.7 38.8 1.0
C8 A:0IH301 2.7 38.6 1.0
C6 A:0IH301 2.7 38.6 1.0
CE1 A:TYR104 3.2 39.1 1.0
N A:ARG108 3.3 33.6 1.0
CA A:ARG108 3.3 36.8 1.0
CZ A:TYR104 3.4 40.4 1.0
CB A:ARG108 3.5 38.0 1.0
CD1 A:TYR104 3.5 37.3 1.0
C A:SER107 3.6 32.3 1.0
CB A:SER107 3.7 29.8 1.0
OH A:TYR104 3.9 44.3 1.0
CD B:ARG108 3.9 46.5 1.0
CE2 A:TYR104 3.9 38.8 1.0
C9 A:0IH301 4.0 38.8 1.0
C5 A:0IH301 4.0 39.0 1.0
CG A:TYR104 4.0 34.8 1.0
O A:TYR104 4.0 28.5 1.0
O A:SER107 4.0 33.2 1.0
NE B:ARG108 4.1 52.3 1.0
CD2 A:TYR104 4.2 37.0 1.0
CA A:SER107 4.3 29.1 1.0
C4 A:0IH301 4.5 39.4 1.0
CG B:ARG108 4.5 42.0 1.0
C A:ARG108 4.8 39.9 1.0
CG A:ARG108 4.8 41.6 1.0
CZ B:ARG108 4.9 55.6 1.0
OG A:SER107 4.9 29.9 1.0
C A:TYR104 4.9 28.9 1.0
CA A:TYR104 5.0 28.2 1.0

Chlorine binding site 2 out of 6 in 8gyd

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Chlorine binding site 2 out of 6 in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:36.2
occ:1.00
 CL2 A:0IH301 0.0 36.2 1.0
C15 A:0IH301 1.7 35.2 1.0
C14 A:0IH301 2.8 34.5 1.0
S1 A:0IH301 2.9 35.0 1.0
OG A:SER107 3.2 29.9 1.0
O A:HOH453 3.4 36.2 1.0
NE2 A:GLN204 3.6 36.6 1.0
C A:GLY12 3.6 25.0 1.0
NH2 A:ARG103 3.6 27.5 1.0
CD2 A:LEU13 3.7 27.5 1.0
CA A:GLY12 3.7 25.9 1.0
N A:LEU13 3.7 24.3 1.0
CZ A:ARG103 3.9 27.1 1.0
C13 A:0IH301 4.0 33.9 1.0
CG A:LEU13 4.0 26.3 1.0
NH1 A:ARG103 4.1 26.8 1.0
O A:GLY12 4.1 24.9 1.0
C12 A:0IH301 4.2 35.1 1.0
OE1 A:GLN204 4.2 33.1 1.0
CD A:GLN204 4.2 35.1 1.0
CA A:LEU13 4.3 23.6 1.0
CB A:SER107 4.4 29.8 1.0
O A:LEU203 4.6 31.3 1.0
NE A:ARG103 4.7 26.2 1.0
CB A:LEU13 4.8 24.2 1.0
OH A:TYR111 4.8 45.7 1.0
OH A:TYR7 4.9 26.6 1.0
N A:GLY12 5.0 25.3 1.0

Chlorine binding site 3 out of 6 in 8gyd

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Chlorine binding site 3 out of 6 in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:36.4
occ:1.00
 CL1 B:0IH302 0.0 36.4 1.0
C7 B:0IH302 1.7 37.1 1.0
C6 B:0IH302 2.7 38.1 1.0
C8 B:0IH302 2.7 37.5 1.0
N B:ARG108 3.4 32.5 1.0
CE2 A:TYR104 3.6 38.8 1.0
C B:SER107 3.6 31.8 1.0
CB B:SER107 3.6 30.4 1.0
CA B:ARG108 3.7 34.5 1.0
CD2 B:TYR104 3.7 36.8 1.0
CG B:ARG108 3.8 42.0 1.0
C9 B:0IH302 4.0 38.3 1.0
C5 B:0IH302 4.0 38.6 1.0
CD A:ARG108 4.0 43.4 1.0
O B:TYR104 4.0 31.3 1.0
O B:SER107 4.0 31.5 1.0
OH A:TYR104 4.0 44.3 1.0
CA B:SER107 4.2 30.4 1.0
CE2 B:TYR104 4.3 38.8 1.0
CZ A:TYR104 4.3 40.4 1.0
CB B:ARG108 4.3 37.2 1.0
C4 B:0IH302 4.5 39.1 1.0
CD2 A:TYR104 4.6 37.0 1.0
NE A:ARG108 4.6 45.7 1.0
CG B:TYR104 4.8 34.9 1.0
OG B:SER107 4.9 30.4 1.0
C B:TYR104 4.9 30.2 1.0
CB B:TYR104 4.9 30.9 1.0
CA B:TYR104 5.0 29.3 1.0

Chlorine binding site 4 out of 6 in 8gyd

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Chlorine binding site 4 out of 6 in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:35.4
occ:1.00
 CL2 B:0IH302 0.0 35.4 1.0
C15 B:0IH302 1.7 35.5 1.0
C14 B:0IH302 2.8 34.7 1.0
S1 B:0IH302 2.9 36.2 1.0
O B:HOH424 3.3 35.7 1.0
OG B:SER107 3.5 30.4 1.0
C B:GLY12 3.5 28.7 1.0
NH2 B:ARG103 3.6 28.1 1.0
N B:LEU13 3.6 27.2 1.0
CA B:GLY12 3.7 29.6 1.0
CD2 B:LEU13 3.7 28.6 1.0
OE1 B:GLN204 3.8 39.1 1.0
O B:HOH499 3.8 40.0 1.0
CZ B:ARG103 3.9 28.7 1.0
O B:GLY12 3.9 28.0 1.0
CG B:LEU13 4.0 27.3 1.0
C13 B:0IH302 4.0 35.3 1.0
NH1 B:ARG103 4.0 28.1 1.0
C12 B:0IH302 4.2 36.2 1.0
CA B:LEU13 4.2 26.6 1.0
NE2 B:GLN204 4.3 31.7 1.0
CD B:GLN204 4.4 37.2 1.0
O B:LEU203 4.6 36.5 1.0
NE B:ARG103 4.6 28.0 1.0
CB B:SER107 4.6 30.4 1.0
CB B:LEU13 4.7 26.2 1.0
N B:GLY12 4.9 30.6 1.0
O B:HOH459 4.9 28.0 1.0
OH B:TYR7 5.0 31.3 1.0

Chlorine binding site 5 out of 6 in 8gyd

Go back to Chlorine Binding Sites List in 8gyd
Chlorine binding site 5 out of 6 in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:50.8
occ:1.00
 CL1 B:0IH303 0.0 50.8 1.0
C7 B:0IH303 1.7 50.4 1.0
C6 B:0IH303 2.7 50.3 1.0
C8 B:0IH303 2.7 50.1 1.0
CE B:LYS64 3.7 45.1 1.0
CL2 B:0IH303 3.7 56.9 1.0
C5 B:0IH303 4.0 50.5 1.0
C9 B:0IH303 4.0 50.0 1.0
NZ B:LYS64 4.3 46.4 1.0
C4 B:0IH303 4.5 50.4 1.0
C15 B:0IH303 4.9 57.3 1.0
O B:LEU48 4.9 44.2 1.0
S1 B:0IH303 5.0 56.6 1.0

Chlorine binding site 6 out of 6 in 8gyd

Go back to Chlorine Binding Sites List in 8gyd
Chlorine binding site 6 out of 6 in the Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Schistosoma Japonicum Glutathione S-Transferase Bound with the Ligand Complex of 16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:56.9
occ:1.00
 CL2 B:0IH303 0.0 56.9 1.0
C15 B:0IH303 1.7 57.3 1.0
C14 B:0IH303 2.8 57.5 1.0
S1 B:0IH303 3.0 56.6 1.0
C6 B:0IH303 3.4 50.3 1.0
O B:GLU47 3.4 46.4 1.0
C7 B:0IH303 3.7 50.4 1.0
CL1 B:0IH303 3.7 50.8 1.0
C13 B:0IH303 4.0 57.3 1.0
C12 B:0IH303 4.1 56.8 1.0
C5 B:0IH303 4.2 50.5 1.0
CA B:LEU48 4.4 44.5 1.0
C B:GLU47 4.6 45.8 1.0
C8 B:0IH303 4.6 50.1 1.0
C B:LEU48 4.7 43.8 1.0
O B:LEU48 4.8 44.2 1.0
N B:LEU48 5.0 45.2 1.0

Reference:

X.Wen, M.Zhang, Z.Duan, Y.Suo, W.Lu, R.Jin, B.Mu, K.Li, X.Zhang, L.Meng, Y.Hong, X.Wang, H.Hu, J.Zhu, W.Song, A.Shen, X.Lu. Discovery, Sar Study of Gst Inhibitors From A Novel Quinazolin-4(1 H )-One Focused Dna-Encoded Library. J.Med.Chem. 2023.
ISSN: ISSN 0022-2623
PubMed: 37552553
DOI: 10.1021/ACS.JMEDCHEM.2C02129
Page generated: Thu Dec 28 03:14:48 2023

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