Fluorine in PDB 6gfz: Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B)

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B), PDB code: 6gfz was solved by M.S.Gadd, A.Testa, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.01 / 2.30
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	93.609, 93.609, 364.511, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 24.5

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) also contains other interesting chemical elements:

Arsenic

(As)

12 atoms

The binding sites of Fluorine atom in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) (pdb code 6gfz). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B), PDB code: 6gfz:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:30.6 occ:1.00 FAJ C:EXE301 0.0 30.6 1.0 CBD C:EXE301 1.4 32.1 1.0 CBC C:EXE301 2.3 32.5 1.0 CBF C:EXE301 2.4 36.4 1.0 CAW C:EXE301 2.5 35.0 1.0 OAG C:EXE301 2.7 32.4 1.0 CAQ C:EXE301 2.9 34.8 1.0 OH C:TYR98 3.0 36.6 1.0 CZ C:TYR98 3.0 36.0 1.0 NBG C:EXE301 3.1 41.1 1.0 CE2 C:TYR98 3.2 36.3 1.0 CZ2 C:TRP117 3.3 32.3 1.0 NAS C:EXE301 3.3 30.9 1.0 CH2 C:TRP117 3.3 31.6 1.0 OAI C:EXE301 3.5 27.8 1.0 CAK C:EXE301 3.6 40.4 1.0 CE1 C:TYR98 3.8 37.0 1.0 CD2 C:TYR98 4.1 35.6 1.0 CAP C:EXE301 4.1 36.7 1.0 CAZ C:EXE301 4.2 42.1 1.0 O C:HIS110 4.3 34.0 1.0 C C:EXE301 4.4 46.3 1.0 CAM C:EXE301 4.4 39.8 1.0 CD1 C:TYR98 4.5 35.1 1.0 CE2 C:TRP117 4.5 33.3 1.0 CZ3 C:TRP117 4.6 32.6 1.0 CG C:TRP88 4.7 33.7 1.0 CG C:TYR98 4.7 33.9 1.0 CB C:TRP88 4.8 32.4 1.0 CD2 C:TRP88 4.9 34.9 1.0 O C:EXE301 5.0 45.0 1.0

Fluorine binding site 2 out of 4 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ F:F301 b:35.7 occ:1.00 FAJ F:EXE301 0.0 35.7 1.0 CBD F:EXE301 1.4 37.2 1.0 CBC F:EXE301 2.3 37.7 1.0 CBF F:EXE301 2.4 42.2 1.0 CAW F:EXE301 2.5 36.2 1.0 OAG F:EXE301 2.8 37.4 1.0 CAQ F:EXE301 2.9 40.4 1.0 OH F:TYR98 3.0 39.0 1.0 CZ F:TYR98 3.1 38.1 1.0 NBG F:EXE301 3.1 42.7 1.0 CZ2 F:TRP117 3.2 37.7 1.0 CE2 F:TYR98 3.2 37.8 1.0 NAS F:EXE301 3.3 37.2 1.0 CH2 F:TRP117 3.3 36.4 1.0 OAI F:EXE301 3.5 35.6 1.0 CAK F:EXE301 3.7 49.0 1.0 CE1 F:TYR98 3.9 37.8 1.0 CD2 F:TYR98 4.0 37.5 1.0 CAP F:EXE301 4.2 44.7 1.0 CAZ F:EXE301 4.2 49.8 1.0 O F:HIS110 4.3 43.4 1.0 C F:EXE301 4.3 47.4 1.0 CE2 F:TRP117 4.4 37.5 1.0 CAM F:EXE301 4.5 43.6 1.0 CD1 F:TYR98 4.6 37.1 1.0 CG F:TRP88 4.6 38.0 1.0 CZ3 F:TRP117 4.6 34.5 1.0 CG F:TYR98 4.7 35.3 1.0 CB F:TRP88 4.7 36.8 1.0 CD2 F:TRP88 4.8 40.7 1.0 O F:EXE301 4.9 47.7 1.0 OG F:SER111 4.9 38.4 1.0 CD1 F:TRP88 4.9 37.6 1.0

Fluorine binding site 3 out of 4 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ I:F301 b:34.0 occ:1.00 FAJ I:EXE301 0.0 34.0 1.0 CBD I:EXE301 1.4 32.0 1.0 CBC I:EXE301 2.2 30.6 1.0 CBF I:EXE301 2.4 34.1 1.0 CAW I:EXE301 2.6 31.6 1.0 OAG I:EXE301 2.8 32.4 1.0 CAQ I:EXE301 2.9 33.4 1.0 OH I:TYR98 3.0 37.4 1.0 CZ I:TYR98 3.0 35.8 1.0 NBG I:EXE301 3.1 37.0 1.0 CE2 I:TYR98 3.2 37.0 1.0 CZ2 I:TRP117 3.3 31.8 1.0 NAS I:EXE301 3.3 33.7 1.0 CH2 I:TRP117 3.3 31.1 1.0 OAI I:EXE301 3.5 32.2 1.0 CAK I:EXE301 3.6 38.9 1.0 CE1 I:TYR98 3.8 34.5 1.0 CD2 I:TYR98 4.0 36.5 1.0 O I:HIS110 4.2 36.7 1.0 CAZ I:EXE301 4.2 36.5 1.0 CAP I:EXE301 4.2 37.5 1.0 C I:EXE301 4.4 41.4 1.0 CAM I:EXE301 4.5 39.3 1.0 CD1 I:TYR98 4.5 35.9 1.0 CE2 I:TRP117 4.6 32.6 1.0 CG I:TYR98 4.6 35.5 1.0 CZ3 I:TRP117 4.6 31.1 1.0 CG I:TRP88 4.7 35.3 1.0 CB I:TRP88 4.9 35.1 1.0 CD2 I:TRP88 4.9 34.7 1.0 OG I:SER111 4.9 38.3 1.0 O I:EXE301 5.0 40.3 1.0

Fluorine binding site 4 out of 4 in the Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3S,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14B) within 5.0Å range: probe atom residue distance (Å) B Occ L:F301 b:32.5 occ:1.00 FAJ L:EXE301 0.0 32.5 1.0 CBD L:EXE301 1.4 30.9 1.0 CBC L:EXE301 2.2 30.6 1.0 CBF L:EXE301 2.4 32.5 1.0 CAW L:EXE301 2.6 29.3 1.0 CAQ L:EXE301 2.8 33.7 1.0 OAG L:EXE301 2.9 28.6 1.0 OH L:TYR98 2.9 32.9 1.0 CZ L:TYR98 3.0 33.6 1.0 NBG L:EXE301 3.1 37.6 1.0 CE2 L:TYR98 3.2 36.1 1.0 CZ2 L:TRP117 3.2 25.1 1.0 CH2 L:TRP117 3.2 24.9 1.0 NAS L:EXE301 3.3 32.2 1.0 OAI L:EXE301 3.5 28.0 1.0 CAK L:EXE301 3.6 36.7 1.0 CE1 L:TYR98 3.7 31.5 1.0 CD2 L:TYR98 4.0 35.3 1.0 CAP L:EXE301 4.2 34.3 1.0 O L:HIS110 4.2 35.5 1.0 CAZ L:EXE301 4.2 35.6 1.0 C L:EXE301 4.4 37.6 1.0 CAM L:EXE301 4.5 36.5 1.0 CD1 L:TYR98 4.5 32.0 1.0 CE2 L:TRP117 4.5 25.6 1.0 CZ3 L:TRP117 4.5 25.5 1.0 CG L:TYR98 4.6 32.0 1.0 CG L:TRP88 4.6 31.2 1.0 CB L:TRP88 4.8 29.6 1.0 CD2 L:TRP88 4.8 31.7 1.0 O L:EXE301 4.9 39.5 1.0 CD1 L:TRP88 5.0 31.3 1.0

A.Testa, X.Lucas, G.V.Castro, K.H.Chan, J.E.Wright, A.C.Runcie, M.S.Gadd, W.T.A.Harrison, E.J.Ko, D.Fletcher, A.Ciulli. 3-Fluoro-4-Hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition By the Vhl E3 Ubiquitin Ligase For Targeted Protein Degradation. J. Am. Chem. Soc. V. 140 9299 2018.
ISSN: ESSN 1520-5126
PubMed: 29949369
DOI: 10.1021/JACS.8B05807