Fluorine in PDB 8e5m: Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6

Enzymatic activity of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6

All present enzymatic activity of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6:
3.5.3.1;

Protein crystallography data

The structure of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6, PDB code: 8e5m was solved by R.L.Palte, S.Gathiaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.52 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.47, 286.1, 67.35, 90, 90.32, 90
R / Rfree (%) 19.8 / 23.1

Other elements in 8e5m:

The structure of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 also contains other interesting chemical elements:

Manganese (Mn) 12 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 (pdb code 8e5m). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6, PDB code: 8e5m:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 8e5m

Go back to Fluorine Binding Sites List in 8e5m
Fluorine binding site 1 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:43.2
occ:1.00
 F1 A:UKR1003 0.0 43.2 1.0
C28 A:UKR1003 1.3 42.9 1.0
C29 A:UKR1003 2.3 40.9 1.0
C27 A:UKR1003 2.3 40.3 1.0
C30 A:UKR1003 3.6 38.4 1.0
C26 A:UKR1003 3.6 38.3 1.0
C25 A:UKR1003 4.1 37.6 1.0
O A:HOH1266 4.4 67.8 1.0

Fluorine binding site 2 out of 12 in 8e5m

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Fluorine binding site 2 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1003

b:37.6
occ:1.00
 F A:UKR1003 0.0 37.6 1.0
C14 A:UKR1003 1.3 34.4 1.0
C13 A:UKR1003 2.3 33.9 1.0
C15 A:UKR1003 2.3 32.5 1.0
O A:HOH1162 3.3 34.9 1.0
C12 A:UKR1003 3.6 30.7 1.0
C10 A:UKR1003 3.6 26.4 1.0
O A:THR136 3.7 28.2 1.0
C A:THR136 3.8 28.2 1.0
OG1 A:THR136 3.9 31.7 1.0
N A:SER137 4.0 25.5 1.0
C11 A:UKR1003 4.0 25.2 1.0
CA A:SER137 4.1 24.8 1.0
CB A:THR136 4.1 34.0 1.0
CA A:THR136 4.5 22.0 1.0
CB A:SER137 4.7 26.2 1.0
C9 A:UKR1003 4.8 29.1 1.0

Fluorine binding site 3 out of 12 in 8e5m

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Fluorine binding site 3 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:51.8
occ:1.00
 F1 B:UKR1003 0.0 51.8 1.0
C28 B:UKR1003 1.4 48.6 1.0
C27 B:UKR1003 2.3 46.4 1.0
C29 B:UKR1003 2.3 47.0 1.0
C26 B:UKR1003 3.6 44.9 1.0
C30 B:UKR1003 3.6 45.3 1.0
C25 B:UKR1003 4.1 41.6 1.0

Fluorine binding site 4 out of 12 in 8e5m

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Fluorine binding site 4 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1003

b:38.6
occ:1.00
 F B:UKR1003 0.0 38.6 1.0
C14 B:UKR1003 1.4 37.9 1.0
C15 B:UKR1003 2.3 37.9 1.0
C13 B:UKR1003 2.3 36.9 1.0
O B:HOH1293 3.2 29.1 1.0
O B:THR136 3.3 29.7 1.0
O B:HOH1123 3.5 36.4 1.0
C B:THR136 3.5 29.2 1.0
C12 B:UKR1003 3.6 36.8 1.0
C10 B:UKR1003 3.6 37.7 1.0
N B:SER137 3.8 24.7 1.0
CA B:SER137 3.9 24.1 1.0
CB B:THR136 4.0 34.9 1.0
OG1 B:THR136 4.0 37.8 1.0
C11 B:UKR1003 4.1 37.1 1.0
CA B:THR136 4.3 24.2 1.0
CB B:SER137 4.5 23.8 1.0
O B:HOH1140 4.5 41.7 1.0
C9 B:UKR1003 4.8 35.2 1.0

Fluorine binding site 5 out of 12 in 8e5m

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Fluorine binding site 5 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:61.9
occ:1.00
 F1 C:UKR1003 0.0 61.9 1.0
C28 C:UKR1003 1.4 58.1 1.0
C27 C:UKR1003 2.3 55.7 1.0
C29 C:UKR1003 2.4 55.5 1.0
C26 C:UKR1003 3.6 53.4 1.0
C30 C:UKR1003 3.6 52.8 1.0
C25 C:UKR1003 4.1 50.8 1.0

Fluorine binding site 6 out of 12 in 8e5m

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Fluorine binding site 6 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1003

b:41.2
occ:1.00
 F C:UKR1003 0.0 41.2 1.0
C14 C:UKR1003 1.4 40.0 1.0
C15 C:UKR1003 2.3 38.0 1.0
C13 C:UKR1003 2.4 38.7 1.0
O C:THR136 3.6 30.7 1.0
C12 C:UKR1003 3.6 37.4 1.0
C10 C:UKR1003 3.6 35.1 1.0
C C:THR136 3.8 30.9 1.0
C11 C:UKR1003 4.1 36.5 1.0
N C:SER137 4.1 25.4 1.0
CB C:THR136 4.2 39.3 1.0
CA C:SER137 4.2 24.9 1.0
OG1 C:THR136 4.4 42.0 1.0
CA C:THR136 4.6 26.8 1.0
C9 C:UKR1003 4.9 30.6 1.0
CB C:SER137 4.9 25.6 1.0

Fluorine binding site 7 out of 12 in 8e5m

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Fluorine binding site 7 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1003

b:48.4
occ:1.00
 F1 D:UKR1003 0.0 48.4 1.0
C28 D:UKR1003 1.4 46.2 1.0
C27 D:UKR1003 2.4 44.3 1.0
C29 D:UKR1003 2.4 44.2 1.0
C26 D:UKR1003 3.6 42.8 1.0
C30 D:UKR1003 3.6 42.3 1.0
C25 D:UKR1003 4.1 40.6 1.0

Fluorine binding site 8 out of 12 in 8e5m

Go back to Fluorine Binding Sites List in 8e5m
Fluorine binding site 8 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F1003

b:35.5
occ:1.00
 F D:UKR1003 0.0 35.5 1.0
C14 D:UKR1003 1.4 34.7 1.0
C15 D:UKR1003 2.3 34.1 1.0
C13 D:UKR1003 2.3 33.2 1.0
O D:THR136 3.0 24.5 1.0
C D:THR136 3.3 25.5 1.0
C12 D:UKR1003 3.6 34.1 1.0
C10 D:UKR1003 3.6 34.4 1.0
CB D:THR136 3.7 31.9 1.0
OG1 D:THR136 3.7 37.3 1.0
N D:SER137 3.7 24.0 1.0
CA D:SER137 3.9 23.3 1.0
CA D:THR136 4.0 22.6 1.0
C11 D:UKR1003 4.1 34.5 1.0
CB D:SER137 4.6 24.9 1.0
C9 D:UKR1003 4.8 32.7 1.0
CG2 D:THR136 5.0 30.4 1.0

Fluorine binding site 9 out of 12 in 8e5m

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Fluorine binding site 9 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1003

b:54.7
occ:1.00
 F1 E:UKR1003 0.0 54.7 1.0
C28 E:UKR1003 1.4 52.4 1.0
C29 E:UKR1003 2.3 50.7 1.0
C27 E:UKR1003 2.3 50.8 1.0
C30 E:UKR1003 3.6 47.8 1.0
C26 E:UKR1003 3.6 48.0 1.0
C25 E:UKR1003 4.1 44.8 1.0
O E:HOH1229 4.2 45.4 1.0
O E:HOH1226 4.3 52.8 1.0
O E:HOH1269 4.8 32.9 1.0

Fluorine binding site 10 out of 12 in 8e5m

Go back to Fluorine Binding Sites List in 8e5m
Fluorine binding site 10 out of 12 in the Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Structure of ARG1 Complex with Pyrrolidine-Based Non-Boronic Acid Inhibitor 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1003

b:39.2
occ:1.00
 F E:UKR1003 0.0 39.2 1.0
C14 E:UKR1003 1.4 36.0 1.0
C15 E:UKR1003 2.3 34.5 1.0
C13 E:UKR1003 2.3 35.0 1.0
O E:THR136 3.4 30.6 1.0
C12 E:UKR1003 3.6 33.5 1.0
C10 E:UKR1003 3.6 33.8 1.0
C E:THR136 3.7 31.4 1.0
CB E:THR136 3.9 33.7 1.0
N E:SER137 4.0 29.4 1.0
C11 E:UKR1003 4.1 33.7 1.0
OG1 E:THR136 4.2 39.2 1.0
CA E:SER137 4.3 28.7 1.0
CA E:THR136 4.4 27.6 1.0
CB E:SER137 4.8 30.9 1.0
C9 E:UKR1003 4.8 34.5 1.0

Reference:

S.Gathiaka, R.L.Palte, S.S.So, X.Chai, J.Richard Miller, R.Kuvelkar, J.Wen, S.Cifelli, A.Kreamer, A.Liaw, D.G.Mclaren, C.Fischer. Discovery of Non-Boronic Acid Arginase 1 Inhibitors Through Virtual Screening and Biophysical Methods. Bioorg.Med.Chem.Lett. 29193 2023.
ISSN: ESSN 1464-3405
PubMed: 36822300
DOI: 10.1016/J.BMCL.2023.129193
Page generated: Fri Aug 2 17:49:57 2024

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