Bromine in PDB 8kg5: Prefusion Rsv F Bound to Lonafarnib and D25 Fab

The structure of Prefusion Rsv F Bound to Lonafarnib and D25 Fab also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Bromine atom in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab (pdb code 8kg5). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab, PDB code: 8kg5:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Prefusion Rsv F Bound to Lonafarnib and D25 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Br601 b:94.7 occ:1.00 BR37 A:336601 0.0 94.7 1.0 C29 A:336601 1.9 94.7 1.0 C17 A:336601 2.9 94.7 1.0 C30 A:336601 2.9 94.7 1.0 O A:GLY139 2.9 57.0 1.0 C A:GLY139 3.3 57.0 1.0 CA A:GLY139 3.7 57.0 1.0 N A:PHE140 4.0 56.9 1.0 C35 B:336601 4.1 93.1 1.0 C28 B:336601 4.2 93.1 1.0 C41 A:336601 4.2 94.7 1.0 N32 A:336601 4.2 94.7 1.0 C19 B:336601 4.2 93.1 1.0 C40 B:336601 4.3 93.1 1.0 C20 B:336601 4.3 93.1 1.0 C42 B:336601 4.3 93.1 1.0 C6 B:336601 4.5 93.1 1.0 CA A:PHE140 4.6 56.9 1.0 C39 A:336601 4.7 94.7 1.0 CD A:GLN354 4.7 57.9 1.0 CG A:GLN354 4.8 57.9 1.0 OE1 A:GLN354 4.9 57.9 1.0 NE2 A:GLN354 5.0 57.9 1.0 N A:GLY139 5.0 57.0 1.0

Bromine binding site 2 out of 6 in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Prefusion Rsv F Bound to Lonafarnib and D25 Fab within 5.0Å range: probe atom residue distance (Å) B Occ A:Br601 b:94.7 occ:1.00 BR38 A:336601 0.0 94.7 1.0 C28 A:336601 1.9 94.7 1.0 C35 A:336601 2.8 94.7 1.0 C40 A:336601 3.1 94.7 1.0 C4 A:336601 3.2 94.7 1.0 CD1 A:PHE137 3.2 63.0 1.0 C6 A:336601 3.5 94.7 1.0 C33 A:336601 3.6 94.7 1.0 CA A:PHE137 3.6 63.0 1.0 CE1 A:PHE137 3.9 63.0 1.0 CG A:PHE137 4.0 63.0 1.0 C19 A:336601 4.1 94.7 1.0 CB A:PHE137 4.2 63.0 1.0 N A:PHE137 4.2 63.0 1.0 C42 A:336601 4.3 94.7 1.0 C13 A:336601 4.4 94.7 1.0 O A:PHE137 4.6 63.0 1.0 C A:PHE137 4.6 63.0 1.0 C1 A:336601 4.7 94.7 1.0 C20 A:336601 4.7 94.7 1.0 C39 A:336601 4.7 94.7 1.0 CB C:PHE140 4.7 58.7 1.0 CA C:PHE140 4.8 58.7 1.0 C9 A:336601 4.9 94.7 1.0 CZ A:PHE137 5.0 63.0 1.0 BR37 C:336601 5.0 93.7 1.0

Bromine binding site 3 out of 6 in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Prefusion Rsv F Bound to Lonafarnib and D25 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Br601 b:93.1 occ:1.00 BR37 B:336601 0.0 93.1 1.0 C29 B:336601 1.9 93.1 1.0 C17 B:336601 2.9 93.1 1.0 C30 B:336601 2.9 93.1 1.0 O B:GLY139 3.0 58.3 1.0 C B:GLY139 3.3 58.3 1.0 CA B:GLY139 3.7 58.3 1.0 N B:PHE140 4.0 59.5 1.0 C41 B:336601 4.2 93.1 1.0 N32 B:336601 4.2 93.1 1.0 C35 C:336601 4.3 93.7 1.0 C19 C:336601 4.3 93.7 1.0 C28 C:336601 4.4 93.7 1.0 C20 C:336601 4.4 93.7 1.0 C42 C:336601 4.5 93.7 1.0 C40 C:336601 4.5 93.7 1.0 CD B:GLN354 4.6 62.3 1.0 CA B:PHE140 4.6 59.5 1.0 C39 B:336601 4.7 93.1 1.0 C6 C:336601 4.7 93.7 1.0 CG B:GLN354 4.7 62.3 1.0 OE1 B:GLN354 4.8 62.3 1.0 NE2 B:GLN354 4.8 62.3 1.0 N B:GLY139 4.9 58.3 1.0

Bromine binding site 4 out of 6 in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Prefusion Rsv F Bound to Lonafarnib and D25 Fab within 5.0Å range: probe atom residue distance (Å) B Occ B:Br601 b:93.1 occ:1.00 BR38 B:336601 0.0 93.1 1.0 C28 B:336601 1.9 93.1 1.0 C35 B:336601 2.8 93.1 1.0 C40 B:336601 3.1 93.1 1.0 CD1 B:PHE137 3.2 65.1 1.0 C4 B:336601 3.2 93.1 1.0 C6 B:336601 3.5 93.1 1.0 C33 B:336601 3.6 93.1 1.0 CA B:PHE137 3.7 65.1 1.0 CE1 B:PHE137 3.8 65.1 1.0 CG B:PHE137 4.0 65.1 1.0 C19 B:336601 4.1 93.1 1.0 CB B:PHE137 4.2 65.1 1.0 N B:PHE137 4.3 65.1 1.0 C42 B:336601 4.3 93.1 1.0 C13 B:336601 4.4 93.1 1.0 C B:PHE137 4.7 65.1 1.0 C1 B:336601 4.7 93.1 1.0 O B:PHE137 4.7 65.1 1.0 C20 B:336601 4.7 93.1 1.0 C39 B:336601 4.7 93.1 1.0 CB A:PHE140 4.7 56.9 1.0 CA A:PHE140 4.8 56.9 1.0 C9 B:336601 4.9 93.1 1.0 CZ B:PHE137 4.9 65.1 1.0

Bromine binding site 5 out of 6 in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Prefusion Rsv F Bound to Lonafarnib and D25 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Br601 b:93.7 occ:1.00 BR37 C:336601 0.0 93.7 1.0 C29 C:336601 1.9 93.7 1.0 O C:GLY139 2.8 57.2 1.0 C17 C:336601 2.9 93.7 1.0 C30 C:336601 2.9 93.7 1.0 C C:GLY139 3.1 57.2 1.0 CA C:GLY139 3.6 57.2 1.0 N C:PHE140 3.8 58.7 1.0 C35 A:336601 4.1 94.7 1.0 C28 A:336601 4.2 94.7 1.0 C41 C:336601 4.2 93.7 1.0 N32 C:336601 4.2 93.7 1.0 C19 A:336601 4.2 94.7 1.0 C40 A:336601 4.4 94.7 1.0 CA C:PHE140 4.4 58.7 1.0 C20 A:336601 4.4 94.7 1.0 C42 A:336601 4.5 94.7 1.0 C6 A:336601 4.5 94.7 1.0 C39 C:336601 4.7 93.7 1.0 CD C:GLN354 4.8 58.8 1.0 N C:GLY139 4.9 57.2 1.0 CG C:GLN354 4.9 58.8 1.0 BR38 A:336601 5.0 94.7 1.0

Bromine binding site 6 out of 6 in the Prefusion Rsv F Bound to Lonafarnib and D25 Fab


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Prefusion Rsv F Bound to Lonafarnib and D25 Fab within 5.0Å range: probe atom residue distance (Å) B Occ C:Br601 b:93.7 occ:1.00 BR38 C:336601 0.0 93.7 1.0 C28 C:336601 1.9 93.7 1.0 C35 C:336601 2.8 93.7 1.0 C40 C:336601 3.1 93.7 1.0 CD1 C:PHE137 3.1 60.4 1.0 C4 C:336601 3.2 93.7 1.0 C6 C:336601 3.5 93.7 1.0 CA C:PHE137 3.5 60.4 1.0 C33 C:336601 3.6 93.7 1.0 CE1 C:PHE137 3.7 60.4 1.0 CG C:PHE137 3.8 60.4 1.0 CB C:PHE137 4.0 60.4 1.0 N C:PHE137 4.1 60.4 1.0 C19 C:336601 4.1 93.7 1.0 C42 C:336601 4.3 93.7 1.0 C13 C:336601 4.4 93.7 1.0 O C:PHE137 4.5 60.4 1.0 C C:PHE137 4.5 60.4 1.0 C1 C:336601 4.7 93.7 1.0 C20 C:336601 4.7 93.7 1.0 C39 C:336601 4.7 93.7 1.0 CB B:PHE140 4.8 59.5 1.0 CZ C:PHE137 4.8 60.4 1.0 CA B:PHE140 4.9 59.5 1.0 C9 C:336601 4.9 93.7 1.0 CD2 C:PHE137 4.9 60.4 1.0

Q.Yang, B.Xue, F.Liu, Y.Lu, J.Tang, M.Yan, Q.Wu, R.Chen, A.Zhou, L.Liu, J.Liu, C.Qu, Q.Wu, M.Fu, J.Zhong, J.Dong, S.Chen, F.Wang, Y.Zhou, J.Zheng, W.Peng, J.Shang, X.Chen. Farnesyltransferase Inhibitor Lonafarnib Suppresses Respiratory Syncytial Virus Infection By Blocking Conformational Change of Fusion Glycoprotein. Signal Transduct Target Ther V. 9 144 2024.
ISSN: ESSN 2059-3635
PubMed: 38853183
DOI: 10.1038/S41392-024-01858-5