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Fluorine in PDB 8v1l: Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule

Enzymatic activity of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule

All present enzymatic activity of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule:
3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule, PDB code: 8v1l was solved by M.P.Hughes, J.P.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.87 / 2.68
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.17, 84.69, 102.15, 90, 91.26, 90
R / Rfree (%) 27.6 / 39.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule (pdb code 8v1l). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule, PDB code: 8v1l:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8v1l

Go back to Fluorine Binding Sites List in 8v1l
Fluorine binding site 1 out of 6 in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:59.5
occ:1.00
 F1 A:Y9M201 0.0 59.5 1.0
C5 A:Y9M201 1.4 51.4 1.0
C4 A:Y9M201 2.4 52.1 1.0
C6 A:Y9M201 2.4 46.7 1.0
N2 A:Y9M201 2.5 46.8 1.0
C7 A:Y9M201 2.8 45.7 1.0
C9 A:Y9M201 2.8 45.9 1.0
O A:ASN122 3.0 45.3 1.0
C10 A:Y9M201 3.0 45.0 1.0
O2 A:Y9M201 3.5 54.9 1.0
O1 A:Y9M201 3.8 43.9 1.0
C18 A:Y9M201 3.8 42.1 1.0
C3 A:Y9M201 3.8 49.1 1.0
C A:ASN122 3.9 47.6 1.0
C19 A:Y9M201 3.9 41.9 1.0
C2 A:Y9M201 4.0 47.5 1.0
C8 A:Y9M201 4.3 45.5 1.0
CD1 A:PHE124 4.3 34.6 1.0
C17 A:Y9M201 4.4 41.8 1.0
CE1 A:PHE124 4.5 34.7 1.0
C20 A:Y9M201 4.5 44.9 1.0
CA A:ASN122 4.6 50.4 1.0
N A:LYS123 4.8 45.9 1.0
CG1 A:VAL11 4.9 23.9 1.0
C11 A:Y9M201 4.9 49.3 1.0
O3 A:Y9M201 4.9 48.5 1.0
C16 A:Y9M201 5.0 43.2 1.0
N1 A:Y9M201 5.0 47.4 1.0
CA A:LYS123 5.0 43.1 1.0

Fluorine binding site 2 out of 6 in 8v1l

Go back to Fluorine Binding Sites List in 8v1l
Fluorine binding site 2 out of 6 in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F201

b:58.7
occ:1.00
 F1 B:Y9M201 0.0 58.7 1.0
C5 B:Y9M201 1.4 51.7 1.0
C6 B:Y9M201 2.3 48.9 1.0
C4 B:Y9M201 2.4 52.9 1.0
N2 B:Y9M201 2.5 48.9 1.0
C8 B:Y9M201 2.7 48.1 1.0
C7 B:Y9M201 2.9 48.4 1.0
O B:ASN122 2.9 57.8 1.0
C B:ASN122 3.4 52.3 1.0
O2 B:Y9M201 3.5 56.5 1.0
O1 B:Y9M201 3.7 45.1 1.0
C3 B:Y9M201 3.7 45.5 1.0
C2 B:Y9M201 3.8 48.2 1.0
C9 B:Y9M201 3.9 48.4 1.0
N B:LYS123 4.0 47.6 1.0
CA B:LYS123 4.1 45.5 1.0
C10 B:Y9M201 4.1 47.2 1.0
CA B:ASN122 4.2 54.1 1.0
C20 B:Y9M201 4.3 57.3 1.0
C19 B:Y9M201 4.3 55.2 1.0
CD1 B:PHE124 4.4 33.2 1.0
O3 B:Y9M201 4.5 41.5 1.0
CB B:ASN122 4.5 54.1 1.0
C21 B:Y9M201 4.6 56.9 1.0
C18 B:Y9M201 4.6 56.2 1.0
N1 B:Y9M201 4.7 49.4 1.0
C11 B:Y9M201 4.7 40.5 1.0
CE1 B:PHE124 4.9 33.5 1.0
N B:PHE124 4.9 35.6 1.0
C16 B:Y9M201 4.9 54.4 1.0
C17 B:Y9M201 5.0 55.7 1.0
C B:LYS123 5.0 42.9 1.0

Fluorine binding site 3 out of 6 in 8v1l

Go back to Fluorine Binding Sites List in 8v1l
Fluorine binding site 3 out of 6 in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:53.4
occ:1.00
 F1 C:Y9M201 0.0 53.4 1.0
C5 C:Y9M201 1.4 54.8 1.0
C6 C:Y9M201 2.4 53.6 1.0
C4 C:Y9M201 2.4 56.4 1.0
O C:ASN122 2.8 66.9 1.0
N2 C:Y9M201 3.0 56.0 1.0
O C:HOH305 3.1 34.8 1.0
O2 C:Y9M201 3.2 59.3 1.0
C7 C:Y9M201 3.7 53.6 1.0
C8 C:Y9M201 4.0 53.3 1.0
C C:ASN122 4.0 68.6 1.0
C3 C:Y9M201 4.4 55.8 1.0
CB C:ASN122 4.5 69.3 1.0
C9 C:Y9M201 4.6 52.9 1.0
O3 C:Y9M201 4.7 55.8 1.0
C10 C:Y9M201 4.7 53.4 1.0
CA C:ASN122 4.9 73.0 1.0
N C:LYS123 5.0 61.7 1.0

Fluorine binding site 4 out of 6 in 8v1l

Go back to Fluorine Binding Sites List in 8v1l
Fluorine binding site 4 out of 6 in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F201

b:45.7
occ:1.00
 F1 D:Y9M201 0.0 45.7 1.0
C5 D:Y9M201 1.4 42.1 1.0
C4 D:Y9M201 2.4 41.6 1.0
C6 D:Y9M201 2.4 41.2 1.0
N2 D:Y9M201 2.6 39.6 1.0
O D:ASN122 2.8 45.0 1.0
C9 D:Y9M201 2.9 41.9 1.0
C7 D:Y9M201 3.0 41.3 1.0
C19 D:Y9M201 3.4 34.5 1.0
O2 D:Y9M201 3.4 40.1 1.0
C20 D:Y9M201 3.6 35.5 1.0
C10 D:Y9M201 3.6 42.0 1.0
O1 D:Y9M201 3.7 43.1 1.0
C D:ASN122 3.8 49.7 1.0
C3 D:Y9M201 3.8 40.4 1.0
C18 D:Y9M201 3.9 37.0 1.0
C2 D:Y9M201 4.0 40.6 1.0
CD1 D:PHE124 4.0 32.1 1.0
C21 D:Y9M201 4.2 34.6 1.0
CE1 D:PHE124 4.4 31.3 1.0
C8 D:Y9M201 4.4 42.7 1.0
N D:LYS123 4.5 49.9 1.0
C17 D:Y9M201 4.5 37.6 1.0
CA D:LYS123 4.6 50.6 1.0
CB D:ASN122 4.7 47.5 1.0
C16 D:Y9M201 4.7 35.3 1.0
CA D:ASN122 4.7 50.0 1.0
N D:PHE124 4.9 45.3 1.0
O3 D:Y9M201 4.9 40.9 1.0
N1 D:Y9M201 4.9 39.3 1.0
C11 D:Y9M201 4.9 40.5 1.0

Fluorine binding site 5 out of 6 in 8v1l

Go back to Fluorine Binding Sites List in 8v1l
Fluorine binding site 5 out of 6 in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F201

b:51.2
occ:1.00
 F1 E:Y9M201 0.0 51.2 1.0
C5 E:Y9M201 1.4 47.2 1.0
C4 E:Y9M201 2.3 46.7 1.0
C6 E:Y9M201 2.4 45.8 1.0
N2 E:Y9M201 2.5 41.0 1.0
O E:ASN122 2.9 48.4 1.0
C10 E:Y9M201 3.1 45.1 1.0
O1 E:Y9M201 3.2 45.3 1.0
C7 E:Y9M201 3.2 44.9 1.0
C E:ASN122 3.3 44.5 1.0
O2 E:Y9M201 3.5 47.4 1.0
C3 E:Y9M201 3.6 39.9 1.0
C2 E:Y9M201 3.7 41.5 1.0
N E:LYS123 3.7 38.0 1.0
O3 E:Y9M201 3.8 37.3 1.0
CA E:LYS123 4.0 35.7 1.0
C8 E:Y9M201 4.0 41.8 1.0
CE1 E:PHE124 4.2 30.9 1.0
CA E:ASN122 4.2 46.3 1.0
CB E:ASN122 4.3 47.3 1.0
CD1 E:PHE124 4.3 29.1 1.0
C11 E:Y9M201 4.4 38.0 1.0
C20 E:Y9M201 4.5 36.5 1.0
C9 E:Y9M201 4.5 46.2 1.0
C19 E:Y9M201 4.8 35.9 1.0
C21 E:Y9M201 4.9 35.1 1.0
N1 E:Y9M201 4.9 38.8 1.0
CB E:LYS123 5.0 37.4 1.0

Fluorine binding site 6 out of 6 in 8v1l

Go back to Fluorine Binding Sites List in 8v1l
Fluorine binding site 6 out of 6 in the Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the NTF2L Domain of Human G3BP1 in Complex with Small Molecule within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F201

b:47.0
occ:1.00
 F1 F:Y9M201 0.0 47.0 1.0
C5 F:Y9M201 1.4 42.7 1.0
C4 F:Y9M201 2.4 38.7 1.0
C6 F:Y9M201 2.4 41.3 1.0
N2 F:Y9M201 3.0 34.9 1.0
O2 F:Y9M201 3.2 40.3 1.0
C7 F:Y9M201 3.2 40.0 1.0
O F:ASN122 3.3 41.7 1.0
C9 F:Y9M201 3.4 38.8 1.0
O F:HOH327 3.5 24.7 1.0
CB F:ASN122 3.5 45.0 1.0
C10 F:Y9M201 3.6 39.3 1.0
C3 F:Y9M201 4.3 33.6 1.0
C F:ASN122 4.3 42.4 1.0
C13 F:Y9M201 4.3 34.6 1.0
O3 F:Y9M201 4.3 35.8 1.0
CG F:ASN122 4.4 44.7 1.0
CA F:ASN122 4.5 43.5 1.0
C11 F:Y9M201 4.6 35.1 1.0
C8 F:Y9M201 4.6 40.8 1.0
ND2 F:ASN122 5.0 43.7 1.0

Reference:

B.D.Freibaum, J.Messing, H.Nakamura, U.Yurtsever, J.Wu, H.J.Kim, J.Hixon, R.M.Lemieux, J.Duffner, W.Huynh, K.Wong, M.White, C.Lee, R.E.Meyers, R.Parker, J.P.Taylor. Identification of Small Molecule Inhibitors of G3BP-Driven Stress Granule Formation. J.Cell Biol. V. 223 2024.
ISSN: ESSN 1540-8140
PubMed: 38284934
DOI: 10.1083/JCB.202308083
Page generated: Wed Jul 16 09:32:24 2025

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