Fluorine in PDB 5o48: P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound

All present enzymatic activity of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound:
2.3.1.97;

The structure of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound, PDB code: 5o48 was solved by J.A.Brannigan, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	100.67 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.565, 121.983, 178.247, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20

The structure of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound also contains other interesting chemical elements:

Magnesium	(Mg)	3 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Fluorine atom in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound (pdb code 5o48). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound, PDB code: 5o48:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:17.4 occ:1.00 F A:9K2502 0.0 17.4 1.0 C13 A:9K2502 1.4 14.9 1.0 C14 A:9K2502 2.4 14.3 1.0 C12 A:9K2502 2.4 15.5 1.0 N A:ALA366 3.3 7.4 1.0 CB A:ASN365 3.3 9.6 1.0 C A:ALA366 3.5 8.1 1.0 C A:ASN365 3.5 7.7 1.0 CA A:ALA366 3.6 8.2 1.0 O A:ALA366 3.6 8.1 1.0 CB A:TYR211 3.7 10.5 1.0 O A:HOH683 3.7 10.9 1.0 C15 A:9K2502 3.7 15.9 1.0 C11 A:9K2502 3.7 12.5 1.0 O A:ASN365 3.8 8.2 1.0 CD2 A:TYR334 3.9 7.4 1.0 N A:LEU367 3.9 7.1 1.0 CA A:ASN365 3.9 7.7 1.0 CE2 A:TYR334 4.1 7.8 1.0 CG A:LEU367 4.2 7.8 1.0 C10 A:9K2502 4.2 14.5 1.0 O A:HOH750 4.3 19.2 1.0 CD2 A:LEU367 4.4 8.8 1.0 CG A:ASN365 4.5 9.3 1.0 O A:TYR212 4.5 10.4 1.0 CA A:TYR211 4.6 9.7 1.0 CA A:LEU367 4.7 7.8 1.0 CG A:TYR211 4.7 12.0 1.0 N A:TYR212 4.9 9.5 1.0 C16 A:9K2502 4.9 14.4 1.0 CG A:TYR334 5.0 7.0 1.0 CB A:LEU367 5.0 7.6 1.0

Fluorine binding site 2 out of 3 in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:16.0 occ:1.00 F B:9K2502 0.0 16.0 1.0 C13 B:9K2502 1.3 12.8 1.0 C12 B:9K2502 2.3 11.5 1.0 C14 B:9K2502 2.4 13.8 1.0 CB B:ASN365 3.3 8.9 1.0 N B:ALA366 3.3 7.6 1.0 C B:ASN365 3.4 7.4 1.0 C B:ALA366 3.5 7.3 1.0 C15 B:9K2502 3.6 14.5 1.0 CB B:TYR211 3.6 8.9 1.0 C11 B:9K2502 3.6 11.9 1.0 CA B:ALA366 3.6 7.4 1.0 O B:ALA366 3.7 7.2 1.0 O B:HOH690 3.8 12.3 1.0 O B:ASN365 3.8 8.0 1.0 CA B:ASN365 3.9 7.6 1.0 CD2 B:TYR334 4.0 8.1 1.0 N B:LEU367 4.0 6.4 1.0 CE2 B:TYR334 4.0 7.6 1.0 C10 B:9K2502 4.1 11.6 1.0 CG B:LEU367 4.2 6.8 1.0 CG B:ASN365 4.4 10.4 1.0 O B:HOH770 4.4 18.1 1.0 O B:TYR212 4.5 8.6 1.0 CD2 B:LEU367 4.5 6.8 1.0 CA B:TYR211 4.6 8.1 1.0 CG B:TYR211 4.6 9.0 1.0 CA B:LEU367 4.8 7.1 1.0 C16 B:9K2502 4.8 13.8 1.0 N B:TYR212 4.9 8.6 1.0

Fluorine binding site 3 out of 3 in the P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of P.Vivax Nmt with An Aminomethylindazole Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:20.4 occ:1.00 F C:9K2502 0.0 20.4 1.0 C13 C:9K2502 1.4 19.5 1.0 C14 C:9K2502 2.4 18.3 1.0 C12 C:9K2502 2.4 16.6 1.0 N C:ALA366 3.3 10.0 1.0 CB C:ASN365 3.3 14.6 1.0 C C:ASN365 3.4 12.7 1.0 C C:ALA366 3.5 10.2 1.0 O C:ALA366 3.6 12.7 1.0 CB C:TYR211 3.6 12.8 1.0 C15 C:9K2502 3.6 21.6 1.0 CA C:ALA366 3.7 9.7 1.0 C11 C:9K2502 3.7 15.9 1.0 O C:HOH760 3.8 14.4 1.0 O C:ASN365 3.8 12.3 1.0 CA C:ASN365 3.9 12.4 1.0 CD2 C:TYR334 3.9 9.6 1.0 N C:LEU367 4.0 10.8 1.0 CE2 C:TYR334 4.1 10.4 1.0 C10 C:9K2502 4.2 17.5 1.0 CG C:LEU367 4.3 9.0 1.0 CG C:ASN365 4.3 18.7 1.0 O C:TYR212 4.4 13.1 1.0 CD2 C:LEU367 4.5 9.6 1.0 O C:HOH632 4.6 20.2 1.0 CA C:TYR211 4.6 11.2 1.0 CG C:TYR211 4.7 13.5 1.0 CA C:LEU367 4.8 9.4 1.0 N C:TYR212 4.8 12.0 1.0 OD1 C:ASN365 4.8 18.4 1.0 C16 C:9K2502 4.8 21.8 1.0 ND2 C:ASN365 5.0 20.4 1.0

A.Mousnier, A.S.Bell, D.P.Swieboda, J.Morales-Sanfrutos, I.Perez-Dorado, J.A.Brannigan, J.Newman, M.Ritzefeld, J.A.Hutton, A.Guedan, A.S.Asfor, S.W.Robinson, I.Hopkins-Navratilova, A.J.Wilkinson, S.L.Johnston, R.J.Leatherbarrow, T.J.Tuthill, R.Solari, E.W.Tate. Fragment-Derived Inhibitors of Human N-Myristoyltransferase Block Capsid Assembly and Replication of the Common Cold Virus. Nat Chem V. 10 599 2018.
ISSN: ESSN 1755-4349
PubMed: 29760414
DOI: 10.1038/S41557-018-0039-2