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

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A), PDB code: 6gfy 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)	49.36 / 2.70
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	94.115, 94.115, 367.972, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 25.8

The structure of Pvhl:Elob:Eloc in Complex with Modified VH032 Containing (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) 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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) (pdb code 6gfy). 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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A), PDB code: 6gfy:
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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A)


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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:32.0 occ:1.00 FAJ C:EXH301 0.0 32.0 1.0 CBD C:EXH301 1.3 31.9 1.0 CBC C:EXH301 2.3 32.2 1.0 CBF C:EXH301 2.4 33.2 1.0 OAI C:EXH301 2.6 30.3 1.0 CAW C:EXH301 3.1 33.0 1.0 O C:HIS110 3.1 35.8 1.0 CZ2 C:TRP117 3.2 29.1 1.0 CA C:SER111 3.2 31.0 1.0 CB C:SER111 3.3 28.1 1.0 OG C:SER111 3.3 26.1 1.0 NAS C:EXH301 3.4 31.5 1.0 NBG C:EXH301 3.5 34.1 1.0 CAQ C:EXH301 3.5 32.8 1.0 C C:HIS110 3.8 36.8 1.0 N C:SER111 3.8 34.1 1.0 CAK C:EXH301 3.9 37.8 1.0 CD1 C:ILE109 3.9 38.3 1.0 CH2 C:TRP117 3.9 29.8 1.0 OAG C:EXH301 3.9 32.5 1.0 CE2 C:TRP117 4.3 28.2 1.0 C C:SER111 4.5 30.9 1.0 CAP C:EXH301 4.6 33.5 1.0 NE1 C:TRP117 4.6 28.5 1.0 CAZ C:EXH301 4.6 37.3 1.0 CAM C:EXH301 4.6 36.7 1.0 OH C:TYR98 4.7 30.8 1.0 C C:EXH301 4.7 32.9 1.0 CE2 C:TYR98 4.9 31.8 1.0 N C:TYR112 5.0 31.4 1.0 CZ C:TYR98 5.0 31.0 1.0

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


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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ F:F301 b:35.5 occ:1.00 FAJ F:EXH301 0.0 35.5 1.0 CBD F:EXH301 1.3 33.9 1.0 CBC F:EXH301 2.4 33.2 1.0 CBF F:EXH301 2.4 36.0 1.0 OAI F:EXH301 2.7 29.7 1.0 CAW F:EXH301 3.1 36.0 1.0 CZ2 F:TRP117 3.2 31.0 1.0 O F:HIS110 3.3 32.8 1.0 OG F:SER111 3.3 27.1 1.0 NAS F:EXH301 3.3 36.2 1.0 CA F:SER111 3.4 29.9 1.0 CB F:SER111 3.4 28.1 1.0 NBG F:EXH301 3.5 36.3 1.0 CAQ F:EXH301 3.6 33.3 1.0 CAK F:EXH301 3.8 39.6 1.0 CH2 F:TRP117 3.9 31.2 1.0 C F:HIS110 4.0 33.3 1.0 OAG F:EXH301 4.0 32.3 1.0 N F:SER111 4.0 31.3 1.0 CD1 F:ILE109 4.1 32.0 1.0 CE2 F:TRP117 4.2 29.6 1.0 CAP F:EXH301 4.6 39.0 1.0 CAZ F:EXH301 4.6 41.7 1.0 NE1 F:TRP117 4.6 29.3 1.0 CAM F:EXH301 4.6 39.5 1.0 OH F:TYR98 4.7 32.5 1.0 C F:SER111 4.7 30.6 1.0 C F:EXH301 4.7 35.4 1.0 CE2 F:TYR98 4.8 31.4 1.0 CZ F:TYR98 4.8 31.4 1.0

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


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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ I:F301 b:33.5 occ:1.00 FAJ I:EXH301 0.0 33.5 1.0 CBD I:EXH301 1.4 35.0 1.0 CBC I:EXH301 2.4 34.3 1.0 CBF I:EXH301 2.4 36.7 1.0 OAI I:EXH301 2.6 30.1 1.0 CAW I:EXH301 3.1 37.5 1.0 OG I:SER111 3.2 28.3 1.0 O I:HIS110 3.2 32.1 1.0 CB I:SER111 3.3 29.7 1.0 CA I:SER111 3.3 31.8 1.0 NAS I:EXH301 3.3 35.4 1.0 CZ2 I:TRP117 3.3 25.9 1.0 NBG I:EXH301 3.6 35.8 1.0 CAQ I:EXH301 3.6 35.8 1.0 CAK I:EXH301 3.8 37.4 1.0 C I:HIS110 3.9 34.2 1.0 N I:SER111 3.9 32.7 1.0 CH2 I:TRP117 4.0 26.1 1.0 OAG I:EXH301 4.1 37.5 1.0 CD1 I:ILE109 4.2 33.6 1.0 CE2 I:TRP117 4.3 26.4 1.0 C I:SER111 4.5 32.7 1.0 CAP I:EXH301 4.5 34.5 1.0 CAZ I:EXH301 4.5 36.6 1.0 CAM I:EXH301 4.6 37.5 1.0 NE1 I:TRP117 4.6 26.7 1.0 OH I:TYR98 4.7 31.3 1.0 C I:EXH301 4.8 34.7 1.0 CE2 I:TYR98 4.8 33.0 1.0 CZ I:TYR98 4.9 31.4 1.0 N I:TYR112 4.9 31.8 1.0

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


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 (3R,4S)-3- Fluoro-4-Hydroxyproline (Ligand 14A) within 5.0Å range: probe atom residue distance (Å) B Occ L:F301 b:28.4 occ:1.00 FAJ L:EXH301 0.0 28.4 1.0 CBD L:EXH301 1.4 30.2 1.0 CBC L:EXH301 2.4 30.8 1.0 CBF L:EXH301 2.4 31.5 1.0 OAI L:EXH301 2.6 27.8 1.0 OG L:SER111 3.1 28.4 1.0 CB L:SER111 3.1 30.8 1.0 CAW L:EXH301 3.2 31.6 1.0 CA L:SER111 3.3 33.6 1.0 CZ2 L:TRP117 3.3 27.8 1.0 O L:HIS110 3.3 39.7 1.0 NAS L:EXH301 3.4 28.9 1.0 NBG L:EXH301 3.6 33.9 1.0 CAQ L:EXH301 3.6 31.4 1.0 CAK L:EXH301 3.9 32.3 1.0 C L:HIS110 4.0 38.0 1.0 N L:SER111 4.0 35.3 1.0 OAG L:EXH301 4.0 29.9 1.0 CH2 L:TRP117 4.1 27.9 1.0 CD1 L:ILE109 4.2 32.9 1.0 CE2 L:TRP117 4.3 26.8 1.0 NE1 L:TRP117 4.6 27.2 1.0 C L:SER111 4.6 34.6 1.0 CAP L:EXH301 4.7 28.8 1.0 CAZ L:EXH301 4.7 30.8 1.0 CAM L:EXH301 4.7 33.2 1.0 C L:EXH301 4.8 36.2 1.0 OH L:TYR98 4.8 28.0 1.0 CE2 L:TYR98 4.9 28.8 1.0 N L:TYR112 5.0 34.0 1.0 CZ L:TYR98 5.0 27.7 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